Epi Lab Terms

Front 1

cluster

Back 1

a group of strains sharing a unique pattern, marker, or typing information among isolates in a study collection.

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cladistics

Back 2

describes the methods to define evolutionary relationships between organisms based on shared characteristics

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dendrogram

Back 3

an arrangement of taxa in a hierarchic structure, according to the similarity or differences indices.

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taxon

Back 4

a general taxnomic unit defined by a set of characteristics common to each member of that unit (genus, species, sub-species, etc)

Front 5

What is a phylogenetic tree used for?

Back 5

a phylogenetic tree is used to help represent evolutionary relationships between organisms that are believed to have some common ancestry.

**Trees are used in molecular epidemiology for analysis of similarity and relatedness.

Front 6

How do you decide which type of tree to use?

Back 6

The type of epidemiological question being asked defines which classification approach is most appropriate.

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Epid data is the benchmark for ____

Back 7

it is the benchmark for typing method validation and assumptions of pathogen relatedness. Present and recent relationships of pathogens are tested via strain typing methods. i.e. serotyping, PFGE, etc

Front 8

Why are serotypes bad for epidemiological studies?

Back 8

serotypes provide information on evolutionary relationships/organism relatedness over a long period of time. In outbreaks, we need to look over a short period of time.

Front 9

what are some different aspects that you should consider as you get set to build a tree?

Back 9

efficiency, power, consistency/reliability, robustness, are underlying assumptions ever violated

Front 10

What are limitations to the use of trees?

Back 10

trees are meant to provide insight into a research question and not intended to represent an entire species history. Several factors, like gene transfers, may affect the output placed into a tree. Some sources of data are not appropriate for phylogeny studies (i.e. sero-typing data). All knowledge of limitations related to DNA degradation over time must be considrered, especially in the case of evolutionary trees aimed at ancient or extinct organisms.

Front 11

What does each line on a tree represent?

Back 11

It represents one particular organism of interest.

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What is the distance of the lines used to determine?

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Used to determine how closely two organisms are related to one another or how long ago they may have had a common ancestor.

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Bifurcating tree

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has a maximum of 2 descendants arising from each of the interior nodes.

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multifurcating tree

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has multiple descendent arising from each of hte interior nodes.

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rooted vs unrooted tree

Back 15

rooted tree is used to make inferences about the most common ancestor of the branches and how different organisms are related based on the common ancestor. (mainly used for evolutionary studies.

Unrooted trees refer samples to one another not to the original source. (mainly used for epidemiological studies.)

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measures of similarity

Back 16

scaled on a 0-1 or 0%-100%

1 euqals perfect identity.

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swofford equation

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distance = 1 - similarity phenogram vs dendrogram

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phenogram vs dendrogram

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phenograms do not reflect phylogenic relationships - based on observable (morphological differences). So, phenograms can infer epidemiological, but not evolutionary relationships.

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Hierarchic vs. Non-Hierarchic

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hierarchic:
ordered structures, nearest neighbor, furthest neighbor, UPGMA (unweighted pair-group method using arithmetic averages)

Non-hierarchic:
do not assign ranks or orders, taxa are not a subset of a larger, more inclusive taxa

unrooted trees

Front 20

cladistics models for inferring relationships

Back 20

parsimony
maximum likelihood analysis
compatibility analysis
bayesian analysis