Chapter 19: Systematics and Phylogenetics Flashcards

Question

tempo of evolution

Answer 1

- varies within and among lineages - evolutionary changes may accumulate slowly in a lineage as the environment shifts over time - this pattern is called ANAGENESIS - if changes through time are substantial and the fossil record is incomplete, palaeontologists who discover morphologically distinct fossils in different strata may assign them different species: "the ancestral species A evolved into descendant species B"

Answer 2

- pattern where evolutionary changes may accumulate slowly in a lineage as the environment shifts over time - the production of new species through anagenesis doesn't increase biodiversity, but is the simple gradual transformation of one species into another as characteristics shift over time

Answer 3

straight line

Answer 4

when an ancestral species undergoes speciation to produce two descendant species that are both distinct from the common ancestor - does increase biodiversity

Answer 5

- branching pattern, with 2 descendants arising from their common ancestor - when they first emerge, the two branches may represent new species but as cladogenesis continues repeatedly, branches will form branchlets and twigs, each of the new species may become the common ancestor of its own many descendants. - therefore, each new species produced by cladogenesis has the potential to become the "root" of its own evolutionary lineage

Answer 6

each branching point on a phylogenetic tree

Answer 7

each node with all the branches, branchlets, and twigs, that emerge from it - some clades includes thousands of species (aves,birds) whereas others include a few (geospiza, ground+cactus finches)

Answer 8

nested within larger and older clades

Answer 9

sister clades/sister taxa - because they are each other's closest relatives

Answer 10

sister species

Answer 11

monophyletic taxa (comprises 1 clade, an ancestral species (represented by a node) and all of its descendants but no other species) - monophyletic taxa are defined at every level of the taxonomic hierarchy (i.e. all cat species are the only descendants of a common ancestor, therefore Feliade is one small, but complete branch on the Tree of Life)

Answer 12

a) DEPICTION OF TIME: - position of the nodes reveal when a scale originated (if it has a explicit axis) - the length of the branch between nodes indexes how long an ancestral group persisted before it diversified - time scale usually isn't precise or specified - sequence of nodes indicates the order in which clads appeared; the lengths of the branches contain no specific information about the time since 2 clades diverged b) DEPICTION OF RELATEDNESS - vertical spacing doesn't indicate relatedness - the vertical axis label will describe how the spacing should be interpreted c) NO. OF DESCENDENTS - most nodes have 2 branches emerging from them, reflecting the evolution of 2 descendants from one ancestor - when biologists have not discovered the pattern of branching, you'll see more branches, these nodes are "unresolved" d) RELATIVE AGES OF CLADES - clades are arranged from oldest (top) to youngest (bottom) - any clade can be rotated around a node without changing the meaning of the phylogenetic tree - when reading the tree, focus on the clades that share more recent common ancestors (indicated by the relative position of the nodes from which they emerge)

Answer 13

how recently sister clades diverged - clades that emerge from a recent common node are more closely related to each other than clades that emerged from an older node

Answer 14

includes an ancestral species and all of its descendants i.e. Dinosauria

Answer 15

includes species from different evolutionary lineages (clades) - most recent common ancestor is not included i.e. birds and bats - 2 clades of vertebrae capable of flight - doesn't include their last common ancestor (4 legged creature that lived millions of years before)

Answer 16

includes an ancestral species and only SOME of its descendants - therefore some descendants are excluded i.e. terrestrial dinosaurs and birds - terrestrial dinosaurs was a paraphyletic taxon, and birds are the descendants of one group of terrestrial dinosaurs - therefore, the monophyletic taxon Dinosauria must include birds and their nonflying relative

Answer 17

how characteristics arose i.e.: he defined birds as a class of oviparous (egg-laying) animals with feathered bodies, 2 wings, 2 feet, and a bony beak - no other animal have all these characteristics, making birds different from mammals, reptiles, and amphibians

Answer 18

indicators of underlying genetic differences between species and lineages - undergo phylogenetic analyses using organisms and molecular characters (they can use any heritable trait, but ignore phenotypic differences due to environmental variation)

Answer 19

- similarity resulting from shared ancestry i.e. 4 limbs of all tetrapod vertebrates - includes any trait: genetic sequences, anatomical structures, mating behaviours, etc. as long as they inherited it from their common ancestor i.e. STAPES - characters can be homologous but differ greatly among species, especially if their function has changed over time - stapes, a bone in the middle ear of tetrapod vertebrates, evolved from, and is therefore homologous to, a bone that supported the jaw joint from fishes - ancestral function is retained in some modern fishes, but its structure, position, and function are different in tetrapods

Answer 20

- sometimes can appear very similar in appearance i.e. overall form of cacti in America resembles spurges in Africa - these lineages arose independently long after those continents had separated: thus, cactuses and spurges did not inherit their similarities from a shared ancestor

Answer 21

evolution of similar adaptations in distantly related organisms that occupy similar environments

Answer 22

phenotypic similarity that evolved independently in different lineages - often the product of convergent evolution

Answer 23

- analogies or analogous characters

Answer 24

1) homologous structures are similar in anatomical detail and in their relationship to surrounding structures EXAMPLE: BIRDS + BATS - bones in the wings of birds and bats are considered homologous - they include the same structural elements and have similar connections to the rest of the skeleton - the fossil record documents that birds and bats inherited the basic skeletal structure of the forelimb from their most recent common ancestor, a tetrapod vertebrae BUT - large flat surfaces of their wings and flying behaviour are homoplastic - birds have wings made up of feathers, and bats have wings made up of membranous skin - their common ancestor lacked any hint in structures on its forelimbs, was confined to life on the ground - therefore, the flight and some of the anatomical structures that produce it are due to convergent evolution 2) in multicellular organisms, homologous characters grow from the same embryonic tissues + in similar ways during development - systematists have always put great stock in embryological indications of homology on the assumption that evolution has conserved the pattern of embryonic development in related organisms

Answer 25

- reveal remarkable shared similarities in the underlying genetic and cellular mechanisms that have contributed to the evolution of convergent characters in spices that aren't closely related

Answer 26

- structural differences between organisms often reflect underlying genetic differences - morphological characteristics are often clearly preserved in the fossil record allowing the comparison of living species w/ their extinct relatives *morphological traits that are useful in phylogenetic analyses vary from group to group - in flowering plants, the details of a flower anatomy may reveal common ancestry - among vertebrates, the presence/absence of scales, feathers, and fur + structure of the skull and jaw help scientists reconstruct the evolutionary history of major groups

Answer 27

- differences in the number of scales on the backs of lizards in the curvature of a vein in the wings of bees may be good indicators of genetic differentiation that accompanied/followed speciation

Answer 28

provide evidence of evolutionary relationships example: analyses of embryos of vertebrates revealed that they are rather closely related to sea cucumbers, sea stars, and sea urchins, and even more closely related to a group of nearly shapeless marine invertebrates called sea squirts of tunicates

Answer 29

reveal the details of all evolutionary relationships - some salamander species in N.A. differ in relatively few morphological features, even when they are genetically, physiologically and behaviourally distinct - researches cannot easily compare the structures of organisms, such as flatworms and dogs that share few morphological traits

Answer 30

systematists often examine behaviour for clues about their relationships - for example: 2 species of tree frogs commonly occur together in forests of the central and eastern US. both species have bumpy skin and adhesive pads on their toes that let them climb vegetation - they also have grey backs, white bellies, yellowish-orange colouration on their thighs, and large white spots below their eyes HOW DO WE KNOW THE FROGS ARE 2 DIFF SPECIES - during breeding season, males of each species use a distinctive mating call to attract females (so only those in the same species mate) - difference in calls is a pre zygotic, reproductive isolating mechanism - they also have diff chromosome numbers (Chrysoscelis-diploid vs Versicolour-tetraploid) = post zygotic mechanism

Answer 31

- using molecular characters such as the nucleotide base sequences of DNA + RNA - because DNA is inherited, shared changes in molecular sequences: insertions, deletions, or substitutions, provide clues to the evolutionary relationships of organisms

Answer 32

- using PCR technology makes it easy to produce numerous copies of specific segments of DNA for analysis - this technique is effective enough to allow scientists to replicate DNA from fossils and preserved specimens - nuclear DNA is frequently used in phylogenetic analyses

Answer 33

1) they provide abundant data: every base in a nucleic acid can serve as a separate, independent character for analysis 2) many genes have been conserved by evolution, molecular sequences can be compared btwn distantly related organisms that share no organismal characteristics 3) be used to study closely related species with only minor morphological differences - molecular characters have drawbacks though - only 4 alternative character states exist at each position in a DNA or RNA sequence, and only 20 alternative character states at each position in a protein - therefore, this can make it hard to assess the homology of a nucleotide base substitution that appears at the same position in the DNA of 2+ species: organismal characters can be analyzed with embryonic development, details of their function, or their presence in the fossil record but molecular characters have no embryonic development, but allow researches to sample the genome directly and systematists sequence data to analyze phylogenetic relationships that organismal characters were unable to resolve (It can be hard to tell if a DNA change in two species comes from a shared ancestor or happened separately. Physical traits (like body structure) can be studied using development, function, or fossils. But DNA sequences don’t have these features—though they let scientists directly compare genomes and solve evolutionary relationships that physical traits couldn’t.)

Answer 34

- constructed phylogenetic trees and classified organisms by assessing the amount of phenotypic divergence btwn lineages, and the patterns of branching evolution that had produced them - they focused on the products of anagenesis (evolutionary change through the accumulation of new or modified characteristics) + products of cladogenesis (the new species and lineages produced through branching evolution) - thus, their classifications did not always strictly reflect the patterns of branching evolution EXAMPLE: tetrapod vertebrae reveals that amphibian and mammalian lineages each diverged early - remaining lineages collectively called Reptilia, diverged into lizards and snakes and turtles+birds+crocs - therefore, even through crocs have scaly skin and sprawling posture and seem like lizards, they share a more recent common ancestor with birds ## Footnote FOCUSED ON SHARED ANCESTRY AND MORHPHOLOGY

Answer 35

the traditional classification recognizes only 4 classes of tetrapod vertebrae 1) Amphibia 2) Mammalia 3) Reptilia 4) Aves - these groups have equal ranking - Reptilia is paraphyletic | from an ancestor but you dont include all the decsendants of them

Answer 36

- they might've shared a recent common ancestor (as lizards and snakes do) - they may have retained some ancestral characteristics after being separated on diff branches of a phylogenetic tree (as lizards and crocs have) TO AVOID CONFUSION: - use willi hennig (German entomologist) who argued that classifications should be based solely on evolutionary relationships - this approach is called CLADISTICS, and it produces phylogenetic hypotheses and classifications that only reflect the branching pattern of evolution and NOT morphological divergence

Answer 37

each CHARACTER can exist in 2 forms called CHARACTER STATES, evolutionary processes change characters over time from an original, ANCESTRAL CHARACTER STATE to a newer, DERIVED CHARACTER STATE - character states that were present in the ancestors of a clade are considered ancestral; those that are new in descendants are considered derived EXAMPLE: ancient fishes which represent the ancestral vertebrates, had fins, but some descendants, the tetrapods, which appeared much later in the fossil record, have limbs. In this example, fins are the ancestral character state, and limbs are the derived character state

Answer 38

APOMORPHY - and a derived character state found in 2+ species is called a SYNAPOMORPHY - the presence of a synapomorphy among species provides a clue that they may be members of the same clade - once a derived character state becomes established in a species, it's likely to be present in that species' descendants - thus, unless they're lost or replaced, SYNAPOMORPHIES CAN SERVE AS MARKERS FOR MONOPHYLETIC LINEAGES

Answer 39

ONLY IN RELATION for example: - most species of animals lack a vertebral column. However, one animal called, the vertebrates-including fishes, amphibians, reptiles, birds, and mammals-has that structure - therefore, when systematists compare vertebrates to all other animals, the absence of a vertebral column is the ancestral character state, and the presence of a vertebral column is derived

Answer 40

- fossil record - outgroup comparison: helps identify ancestral and derived character states **they compare characters in the INGROUP (the clade under study) to those in an OUTGROUP (one or a few species that are related to the clade but aren't included within it) **

Answer 41

ANCESTRAL DERIVED - because the outgroup and in-group are phylogenetically related, the outgroup comparison allows researchers to hypothesize the root (i.e. the common ancestor share by the outgroup + in-group) example: - most modern butterflies have 6 walking legs - but species in 2 families have 4 walking legs and 2 small non-walking legs - outgroup comparison with other insects not in the butterfly clade shows that most insects have 6 walking legs as adults showing that the 6 walking legs is ancestral and 4 is derived

Answer 42

SHARE DERIVED CHARACTER STATES - ancestral character states are shared by in group and outgroup - but they don't help define the in-group for example: - mammals are a clade, a monophyletic lineage because they have mammary glands, hair, etc. - these ancestral character states don't distinguish them from other tetrapod vertebrates - thus, these shared ancestral character states are not useful in defining the mammal clade

Answer 43

exhibit more molecular synapomorphies than spices from different clades - comparison of sequences in the in-group to those in the outgroup may allow a researcher to define ancestral and derived character states

Answer 44

- identifies and names clades instead of pigeonholing organisms into traditional taxonomic categories

Answer 45

an analysis of 5 species can produce 15 possible phylogenetic trees; an analysis of 50 species can produce 3x10^76

Answer 46

- we expect to see similarities that arise when convergent evolution causes distantly related organisms to evolve similar traits independently - we expect to find differences btwn closely related organisms if NS or some microevolutionary process caused a derived character state to be reversed or lost

Answer 47

PARSIMONY APPROACH (Occam's razor) - the simplest plausible explanation of any phenomenon is the best - if we assume that any complex evolutionary change is an unlikely event, then it is extremely unlikely that the same complex change evolved twice in 1 lineage - the best phylogenetic tree is the one that hypothesizes the smallest number of evolutionary changes needed to account for the distribution of character states within a clade; in effect, this approach minimizes the number of homoplasies in the tree I.E. 6 CHANGES IS FAVOURED OVER 7 CHANGES STATISTICAL APPROACHES - when comparing 2 genome sequences, each base in a strand of DNA can be treated as a character with 4 states (A,G,T,C). - we could perform a parsimony analysis on molecular sequence data to identify the phylogenetic tree that assumes the fewest mutations - but the application is complicated

Answer 48

identify homologous characters and infer their ancestral and derived states

Answer 49

1) there are only 4 possible character states at each position in a nucleic acid, identical changes in nucleotides often arise independently 2) segments of DNA that do not code for proteins are less likely than coding regions to be affected by natural selection, therefore, mutations accumulate faster in non-coding regions causing them to evolve rapidly - may appear to evolve faster than coding regions, potentially suggesting that two species are more distantly related than they actually are based on their coding genes. This discrepancy arises because: 3) because of the degeneracy of the genetic code mutations in the third codon position don't often influence the a.a. composition of the protein for which a gene codes - therefore, they are selectively neutral and accumulate more than mutations in the first or second position 4) nucleotide substitutions are more common than others: TRANSITIONS (the substitution of a purine for another purine, or a pyrimidine for another pyrimidine) occur more frequently than TRANSVERSIONS (substitutions between purines and pyrimidines)

Answer 50

comparing alternative trees with specific models about the rates of evolutionary change in different regions of DNA - tree that is most likely to have produced the observed distribution of molecular character states is the best hypothesis

Answer 51

method to illustrate how phylogenetic trees are constructed from DNA sequence data - calculates the overall proportion of bases that differ between 2 species - the genetic distance between closely related species is smaller than the genetic distance between distantly related species, because the gene pools of closely related species accumulated distinctive mutations for a shorter period of time

Answer 52

genetic change that has occurred since 2 species or clades diverged from their common ancestor - not as powerful as maximum likelihood method, the genetic distance method doesn't depend on assumptions about the evolutionary likelihood of different types of mutations

Answer 53

likely not eliminated as often by NS - if mutations accumulate in these segments at a reasonably constant rate differences in their DNA sequences = MOLECULAR CLOCK (index the time at which 2 species diverged) - large differences imply divergence in the distant past, whereas small differences suggest a more recent common ancestor

Answer 54

for example mtDNA evolves relatively quickly; it is useful for dating evolutionary divergences that occurred within the past few million years. Studies of mtDNA have illuminated aspects of the evolutionary history of humans cpDNA ad genes that encode ribosomal RNA evolve much more slowly, providing information about divergences that evolve much slower providing information about divergences that date back hundreds of millions of years

Answer 55

researchers examine the degree of genetic difference between species in relation to their time of divergence estimated from the fossil record - can be done biogeographically with independent data on when volcanic islands first emerged from the sea or when land masses separated

Answer 56

- compare the characteristics of different species to assess the homology of their similarities and infer where on the phylogenetic tree a particular trait appeared FOR EXAMPLE: birds and crocs - included within archosauria, a clade that also includes non-avian dinosaurs flying vertebrates, and a number of other extinct groyps - crocs and birds share anatomical characteristics, such as a 4 chambered heart and the 1 way flow of air through their lungs - they share behavioural characteristics, including the production of mating calls, nest-building behaviour, and parental care of their young. I.E. female crocs guard their nests and moisten them with urine, and fossils were found of the dinosaurs sitting over their eggs (Mark A. Norell of George Washington University)

Answer 57

- the agent that causes acquired immunodeficiency syndrome in humans - genetic analyses linked it to the lentiviruses (like SIV), which infects monkey and chimp species in Africa - SIV doesn't cause illness in those animals, perhaps because their population developed immunity over exposure *TWO STRAINS OF HIV INFECT HUMANS 1) HIV-1: CENTRAL AFRICA 2) HIV-2: WEST AFRICA* - an analysis by Beatrice Hahn of University of Alabama at Birmingham found 2 major clades of SIV - the clade that infects chimps includes HIV-1, and one of the clades that infect monkeys includes HIV-2 - thus, the 2 strains of HIV apparently originated in nonhuman hosts, scientists suspect that the transmission occurred through hunters butchering bush meat acquiring the virus through cuts on their hands

Answer 58

a clear indicator that all forms of life today share a common ancestor

Answer 59

descendants will be mosaics of unmodified (ancestral) and modified (derived) character states - the derived Staes need to be identified and used to reconstruct the ancestor-dependent relationships (i.e. phylogeny)

Answer 60

- we can never directly observe the relationships, the phylogenetic tree is a hypothesis that can be tested by the examination of more characters

Answer 61

1) shape 2) does it exist 3) size relative to the body example: astrgalus: highest bone in the ankle

Answer 62

"informative character" is a position in a DNA sequence where different species exhibit different nucleotides, providing useful information about evolutionary relationships, while an "uninformative character" is a position where all species have the same nucleotide, offering no information about evolutionary history;

Answer 63

1) identify homologous characters - choosing traits that are comparable 2) determine the order and polarity of the characters - what is it about the trait you need to know 3) code the characters and construct a matrix 4) group by synapomorphies (phylogenetic hypothesis) - right kind of trait 5) solve possible problems (parsimony) 6) collect more data and re-test hypothesis

Answer 64

observable trait of an organism - either come down to organism as MODIFIED or UNMODIFIED *if it changed from parent to kid its DERIVED *if it stays the same throughout many generations is ANCESTRAL *eye colour is a bad example of character because of epigenetic, eye colour can change where you can be born with brown eyes and have it turn blue OR - parents have brown eyes (ancestral) - child has blue eyes (derived)

Answer 65

shared ancestry comparing: - streamlined bodies? whales = mammal sharks = fish - therefore similarities can be due to convergent evolution due to COMMON ENVIRONMENT

Answer 66

a new or derived character state (just the trait by itself) - when an apomorphy is found in 2+ taxa its called a SYNAPOMORPHY

Answer 67

a shared derived character (in 2+ species) - the presence of feathers may be considered a synapomorphy for birds *MAKING A PHYLOGENY* - Q: WHAT DISTINGUISHES BIRDS FROM OTHERS? - feathers=synapamorphic (what species in a world has feathers...only birds) - synapomorphies are used to infer phylogenetic relationships - phylogenetic reconstruction can be viewed as a search for synapomorphies

Answer 68

because they already all hav feathers - you need to know if the trait is synapomorphic

Answer 69

an ancestral character state

Answer 70

shared ancestral character state not specific for a group - NOT helpful for phylogeny - i.e. making a bird phylogeny and using "feathers" as a trait - provide no info in resolving phylogenetic relationships - what is symplesiomorphy at one level of analysis might be synapomorphy at another level of analysis

Answer 71

binary: present in 2 states (present/absent) multistate: they exist in more than 2 different states (colour) - ordered and unordered *assume unordered unless you have DNA that proves otherwise* - multistage characters are often treated as unordered because the evolutionary transformation that has led to their present form in unknown

Answer 72

character polarization (method: out-group comparison)

Answer 73

because both lineages face similar environmental challenges and selective pressures i.e. cactus and spurge - both groups have desert environment with thick, water storing stems, spiny structures that keep animals from eating them - also share photosynthetic processes and both have their stomata open at night

Answer 74

In phylogenetic analysis, an out-group species helps determine which traits (character states) are ancestral (plesiomorphic) and which are derived (apomorphic) for the species being studied (the in-group). Plesiomorphic: If a trait is found in both the out-group and in-group, it’s considered an ancestral trait for the in-group. Apomorphic: If a trait is only found in the in-group and not the out-group, it’s considered a derived trait for the in-group

Answer 75

- the ancestral state is coded as 0 - derived states are coded as 1,2,3,etc.

Answer 76

only 4 possible states for each base in a sequence - 25% chance that a reversal to the previous state will occur each time a change occurs at a particular site in DNA - reversals and convergent evolution=homoplasy

Answer 77

a) HOMOLOGUS OPTION: camera eye evolved early on and then lost 5 times (6 changes) b) CONVERGENT EVOLUTION: camera eye evolved at two points along phylogeny (2 changes) w/ parsimony, convergent

Answer 78

- same genus, same family

Answer 79

phylogenetic tree analyses

Answer 80

evolutionary history

Answer 81

- differences in mutations accumulated in noncoding regions of DNA at a reasonably constant rate

Answer 82

ancestral homologus

Answer 83

the adaptive value of these traits can be explained

Answer 84

the wing skeleton of bird and wing skeleton of a bat

Answer 85

group organisms sharing the largest number of ancestral sequences

Answer 86

- monophyletic taxa or lineages only

Answer 87

a birdlike body may be a result of convergent evolution

Answer 88

they had supportive curticle

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Chapter 19: Systematics and Phylogenetics Flashcards

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