Geometric morphometrics Flashcards
What is morphometrics?
Quantitative analysis of form that encompass size and shape
* Analyses performed on live organisms, museum samples and fossils
- Test hypotheses about factors that influence organismal shape using multivariate statistics
What does morphometrics analyze
- Used to analyse:
- The impact of mutations on shape
- Developmental changes in form
- Covariance between ecological factors and shape - Quantitative-genetic parameters of shape
Morphometrics replacement
Done for centuries as initial classifications relied on morphological differentiation
(taxonomy)
NOW:
- Allozymes & RFLPs - Sequencing
- Microsatellites
- AFLPs
- SNPs
- Gene expressions profiles etc…
* Today, relatedness and taxonomic status determined using genetic methods, where much of the work confirms relationships established using morphometrics
* Genetics now used to infer relationships that were once based purely based on morphology
Morphometrics’ new role
- Species can adapt to local environments
- Morphological traits fit/correlate with environmental gradients
- Clarify important speciation mechanisms such as trophic adaptation, predator avoidance, sexual selection
Traditional Morphometrics methods
based on Distances between features and structural Counts (meristic data)
* Not standardised and often lack of common units
* Measurements not always homologous introducing additional variation and ambiguity
Limits in traditional morphometric methods
the information is not independent and is redundant (overlapping areas of measurement)
Limited in power as the geometry among distances and localized shape changes not considered e.g. eye position relative to dorsal fin insertion
Difficult to interpret and visualise what distance and count differences mean
Geometric Morphometrics
Landmark based technique used to determine:
- Overall differences in morphology (similar to traditional techniques)
- Both overall and specific differences in shape among specimens
* Powerful method that captures both traditional information but also takes the geometric relationship among features into account
* The geometry among landmarks (LM) is never lost from the analyses
Geometric Morphometrics landmarks
- Landmarks (LM): Points of correspondence on each object that match between and
within populations of specimens
Landmark repeatability
LMs found on specimens easily by someone else
can typically be solved by providing LM aids or having pictures with the
LMs used on a typical specimen
Articulated structures such as fins, jaws, legs, or claws often not in a standardised orientation and can introduce errors in shape analyses unless corrected
Landmark coverage
Do the LM cover the area of interest well?
* Compromises can be made to characterise important features among specimens at
the sacrifice of choosing only partially Homologous LMs
Number of shape variables generated is 2K-4, where K is the # LM
Landmark coplanarity
For some 2D images there is potential for distortion due to projection of features in the 3rd dimension
* Such LMs are typically avoided but can be incorporated if consistently oriented by the imaging system
Knowledge of studied taxa
Studied fish in nutrient poor system
* High diversity of similar looking fishes all identified by traditional taxonomy as different species
* Repeating assessments was unsuccessful at recovering the same species
* GM techniques found clear differences in body shape and feeding morphology in these fish adapted to oligotrophic system
Bookstein landmark typology
Landmarks used in most analyses are based on Bookstein LM descriptions
TYPE I = Junction of tissues or centres of convex structures
TYPE II = Min & max curvatures and apex(es)
TYPE III = Extreme points away from features & transpositions
* Types I and II are generally preferred
LM related to Geometric morphometrics
Once placed, all LMs together consist of a single LM configuration /specimen
LM configurations are NOT shape variable because they still include non-shape components
* Only when non-shape components are removed are LM configurations treated as shape variable because only shape information remains in configuration’s geometry
* Achieved by superimposition methods
Superimposition
What To Do:
1- Start off in Configuration Space( just your landmarks,)
2- Pass through Pre-Shape Space
3- Shape Space achieved by Removing the effects of orientation by minimising distances between Landmark Configurations in Multi-Dimensional Pre-Shape Space
4- Now you are in Multi-Dimensional Shape Space! (2K-4 dimensions)
