Supplemental Information Case Study 2: Marsupials Accessing IdentifyLife




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Supplemental Information

  • Case Study 2: Marsupials

  • Accessing IdentifyLife

  • How to Implement PhyloJIVE on your website

  • Algorithms

    • Qualitative Characters

    • Quantitative Characters

    • Character set incongruence

  • References

  • Tables

    • SI Table 1

  • Figures

    • Figure Legend

      • SI Figure 1

      • SI Figure 2

      • SI Figure 3

  • How to use PhyloJIVE

    • Controls and navigation

    • How to upload your data

    • Sample datasets: Acacia phylogeny

    • Sample datasets: Trait data: csv file

Case Study 2: Marsupials

Marsupials are a dominant component of the indigenous mammalian fauna of Australia and New Guinea. We obtained a publically available global species level phylogenetic tree for marsupials from TreeBase (Cardillo et al, 2004). This was uploaded into the ALA implementation of PhyloJIVE1. We selected a clade that includes members of the genus Phalanger. We mapped where specimens were collected in the ALA Spatial Portal. We added a geophysical layer showing the mean warmest temperature for New Guinea. Figure S2 clearly shows that unlike other cuscusoids, genus Phalanger is restricted primarily to the cooler regions and that two species on the IUCN red list may be vulnerable to increased temperatures.

We also selected and mapped the clade containing all macropods. Figure S3 shows differences in distribution coincident with state borders. These probably reflect institutional differences in the intensity of collection efforts, differences in classification regimes, and variability of reporting to the national aggregator. Views such as this can assist in the identification of inconsistencies or insufficiencies in aggregated data sources.


  • Accessing IdentifyLife

IdentifyLife (http://www2.identifylife.org) is a collaborative project that provides means to identify organisms. The online identification keys contain morphological trait matrices that are used to identify specimens. The ALA implementation of PhyloJIVE includes a webservice call to the Wattle interactive plant identification key through IdentifyLife. The Acacia traits dataset can be accessed by PhyloJIVE and the character states mapped on the phylogeny. At present this is the only dataset that is available to the ALA implementation of PhyloJIVE. We have demonstrated the feasibility of this service and are actively seeking additional connections.

If the user is analyzing an Acacia phylogeny they can click on the IdentifyLife button on the Options Tab. PhyloJIVE will send a list of terminals in the tree to the IdentifyLife web services which will return all characters and all character states for all terminal taxa. PhyloJIVE will then reconstruct the ancestral states (see below) at all nodes of the tree. This data is stored in the browser and all new characters will be available in the Character Tab for visualization on the tree.

When uploading an Acacia phylogeny in the ALA implementation the user must insert “acacia’ in the Identify Life Dataset box at the bottom of the Edit Phylogenetic Tree page.


  • How to Implement PhyloJIVE on your website

PhyloJIVE can be integrated with websites that provide access control such as the ALA. With minor modifications to just a few files, this application can be deployed on desktop computer or static website or for any phylogeny, character set, and online data sources. The appearance can be controlled through modification of stylesheets such as PhyloJive.css.

Here are some steps to setup a very simple instance of a PhyloJIVE web application:-



  • Download the archive from github:-
    http://trin.github.io/phyloJIVE/

  • From the folder examples, copy the folder phylojive to a convenient location.

  • Open any of the example files, for example hornworts.html

  • This is a self-contained version of the web application with everything but a few js libraries that are sourced online during initiation.

  • If your online sources respond to requests by name then edit hornworts.html and HornwortsInitPhyloJIVE.js in the folder trees_characters.

  • If your online sources are more complex then edit hornwortPlus.html and HornwortsPlusInitPhyloJIVE.js in the folder trees_characters.

  • Appearance can be altered by editing stylesheets such as PhyloJive.css

  • Change filenames, text and titles as appropriate.

  • Edit either HornwortsInitPhyloJIVE.js or HornwortsPlusInitPhyloJIVE.js substituting a newick formatted tree for the one that appears after the variable tree:

    • The tree must be enclosed in single quotes (‘). Take care to ensure that no taxon names contain quotes. These need to be removed or replaced with escaped quotes.

  • Edit either HornwortsInitPhyloJIVE.js or HornwortsPlusInitPhyloJIVE.js substituting a charjson formatted character set for the one that appears after the variable character:

    • You will find a script to convert character sets formatted in csv to charjson in the scripts folder.

  • Links to online data sources can be customized to appear on click.

  • phylogenyExplorer_init to can have variables such as width, height, align, alignName, lateralise = ladderise, branchLength,branchMultiplier, levelsToShow, firstCharacter



  • Algorithms

Qualitative Characters: Each qualitative character state is considered independently. Fitch’s (1996) algorithm is used with slight modifications to account for multiple character states in tips and the possibility of more than 2 branches per node. First we progress from tip taxa to the roots calculating iteratively for each node i of the tree. This is then used to calculate, i.e. the putative ancestral trait state for each node.

For a tip taxon i, a given character may have n states so simply. We then progress iteratively towards the root of the tree so that for node p with a set of Q immediate descendant nodes, then



We then progress iteratively back from the root to the tips as follows. For the root node r, and then for each node p, a new set is calculated as follows


where ,



p is current node, a is the immediate parent of the current node, and Q is the set of children of the current node.

Quantitative Characters: We adapted formulae for weighted means and standard deviation (Sokal and Rohlf 2012). Each quantitative character state is considered independently. We progress iteratively from tip taxa to the roots. For a given node i, we calculate a phylogenetically weighted node mean, , phylogenetically weighted standard deviation, and the cumulative number of child nodes (or descendants) .

For a tip taxon i with a quantitative character value of v, , and .

We then progress towards the root of the tree. The values for tip taxa are used to calculate, , and for the corresponding to node to which they belong. These are then used in calculations the node which contains it, and so on. At each node, weight is given to the number of descendants for each clade under consideration.

So, for a node taxon p, with q immediate descendants,



.




Character set incongruence: Assessing single characters for signs of incongruence is straightforward. The significance of such trait incongruence depends upon the circumstances, meaning and samples. Incongruencies in a clade traits may indicate real signals which are the result of evolutionary patterns and processes or they can arise from insufficient sampling, insufficient trait coding, errors: regardless, they are informative.

For a qualitative character we calculate the putative ancestral states for that character in the phylogeny as detailed above. For node p, with a set of Q immediate descendant nodes, then if members of a clade are deemed as incongruent for that character.

For quantitative characters, there is no definitive measure for uncontrolled and potentially low sample sizes. We adopted a naive model to indicate potential not definitive incongruences. If the variation of the quantitative character within the clade is greater than expected based on the entire tree OR if the values for the quantitative character within the clade is unlikely – given the range and values of the entire tree THEN there is a potential incongruity. So for any quantitative character we compare the mean () and standard deviation ( ) at each node of the tree with the mean () and standard deviation () for that character for the entire tree. If or then a possible state change is indicated where k = 2. If the node mean differs by than 2 standard deviations from the tree mean for the character state; or the character state is more than 2 standard deviations greater than that of the tree deviations then a incongruence is indicated for that character.

Each character in the set is assessed independently at each node for signs of incongruence. If any one character is incongruent then the node is flagged as potentially incongruent.




  • References

Cardillo,M., et al. (2004) A species-level phylogenetic supertree of marsupials. Journal of Zoology, 264, 11–31.

Fitch,W.M. (1969) Toward defining the course of evolution : minimum change for a specific tree topology. Systematic Zoology 20:406-416.

Maslin,B.R. (2001) Wattle, Acacias of Australia. CSIRO PUBLISHING / Australian Biological Resources Study (ABRS).

Sokal, R.R. and.Ro lf,F.J. 2012. Biometry: the principles and practice of statistics in biological research (4 ed.). New York: W. H. Freeman and Co.



TABLES

Table 1: A Formal description of CharJSON syntax in Extended Backus-Naur Form (EBNF)


CharJSON ::=

begin-CharJSON


'{' ( Taxon ':' CharacterStateList ( ',' Taxon ':' CharacterStateList )* )? '}'

end-CharJSON



CharacterStateList ::=

begin-CharacterStateList

'{' ( Character ':' CharacterState ( ',' Character ':' CharacterState )* )? '}'

end-CharacterStateList


CharacterState ::= booleanArray | numberArray | stringArray


booleanArray ::=

begin-booleanArray

'[' ( boolean ( ',' boolean )* )? ']'

end-booleanArray



numberArray ::=

begin-numberArray

'[' ( number ( ',' number )* )? ']'

end-booleanArray

StringArray ::=

begin-StringArray

'[' ( string ( ',' string )* )? ']'

end-StringArray

where numbers, strings, and Booleans are as defined for JSON



Figures

Figure S1: Case Study I. Maps of Acacia character states from “Identify Life” for the combined data of a 13 species clade. A) The PhyloJIVE view panel and B) the contextual menu. The following character states from Identify Life for the clade were mapped: C) pod curvature, D) median phyllode length, E) the presence of absence of bract scars, F) phyllode shape,and G) pod seed orientation. H) The link to the ALA Spatial Portal. I) Seed orientation viewed in the spatial portal as it co-varies with an index showing relative moisture for the driest quarter.



Figure S2. Case Study II. The phalangers (Cuscuses) are native to Northern Australia and New Guinea. Here we have used a species level phylogeny of the masupial to send the members of this clade to the ALA Spatial Portal where occurrences can be superimposed onto maps with climatic, biological, and geophysical layers. The clade of marsupials is mapped onto the mean temperature of the warmest month climatic layer in the ALA Spatial Portal. The known occurrences of two species on the IUCN red list, Phalanger carmelitae (red) and P. sericeus (yellow) coincide with low summer maximum temperatures and may be vulnerable to climate change. Phalanger carmelitae (red), Phalanger vestitus (orange) Phalanger orientalis (gray), Phalanger sericeus (yellow), Phalanger lullulae (black) Phalanger pelengensis-(pink).


Figure S3. Case Study II. Spatial records for Australian Macropod species sourced from Australian Museums and Collections. In this phylogenetic view, continental patterns of distribution are visible as are state based differences in the intensity of collection efforts, classification, and reporting. Compare how the occurrences of widely distributed species stop abruptly at state borders.

How to use ALA implementation of PhyloJIVE

Two implementations of the PhyloJIVE web application currently exist. They differ primarily in arrangement the graphical user elements such as tabs and styling. Figure 1 shows the first. A button placed above the central view pane can be used to reveal and hide tabs which display information as well as a various controls. Figure 2 shows an alternate form of the web application in which information tabs and controls are always visible. Controls and information tabs are otherwise the same.





Figure 1. PhyloJIVE web with application a resizable central view pane for phylogenies with a) with tabs and controls hidden and b) tabs and controls exposed via a button.



Figure 2. The web application as implemented by the Atlas of Living Australia with tabs which are always visible and a fixed size view pane.

The visualization shows:


i) the phylogeny to a chosen depth
ii) triangles to indicate unexpanded clades which contain members beyond the selected view depth
iii) branch lengths in proportion
iv) character states for taxa at tips and nodes
v) nodes where selected character sets may be disjoint in daughter taxa

Up to ten characters can be visualized. Their states are indicated by a matrix of coloured icons appearing to the left of taxon names. Tree branches (and nodes for common ancestors) are coloured according to the predicted value for the first (chosen) character. The font of taxa is blue where the first character is scored. Same for collapsed clades where all have a value all the first character. Where quantitative characters are chosen and the taxon names subsequently aligned, the characters are presented as a heat map.





Figure 3. A portion of the visualization with names aligned. The first column is a quantitative trait colored in a blue heat map with several - indicating missing data. The second column is a qualitative trait with each character state given a different color. The tree branches are colored according to the character state of the first column character.​

Controls and Navigation

Viewers can navigate the screen with the arrow buttons or click and drag with a mouse. The tree can be expanded with the +/- and home key.

Mousing-over a node or name shows the names of the selected characters and their values. The colored icons next to the scientific names represent different values for the three “characters” selected (these can be changed in the “character” tab), as shown in the legend panel on the right. Tree branches (and nodes for common ancestors) are colored according to the predicted value for the first (chosen) character, as calculated using reverse parsimony. Mousing-over a node or name shows the names of the selected characters and their values. Clicking on a node or name brings up a menu to allow the user to perform a number of tasks. PhyloJIVE’s screen is in two sections. The left side window holds the phylogenetic tree and the right side controls the options. By hovering the mouse over the tree, various options become available, by either right or left clicking. These options can be changed on the right hand widow.

Options appear for the use by either a left click or hovering. A left click over a terminal or a node brings up the popup box above. After selecting External links a popup window appears and the use links out to a popup window that as currently programmed links to the species information for the chosen terminal at various webservices including ALA. Australian Plant Image Index, Australian Plant Name Index and EOL. The user can toggle through these windows with the arrow buttons on the lower left window and exit by clicking the x in the lower right. Additional webservices can be accessed by changing the code. If the user selects View Map a distribution map for that terminal or node is generated in the Map box on the right (see below).

If a clade is condensed to a triangle the clade is expanded by selecting Expand/Collapse.

Hover or click on nodes will fetch taxon specific information pulled from pre-configured webservices. Mousing-over a node or name shows the names of the selected characters and their values (see below). Left clicking on a node or name brings up a menu to allow the user to perform a number of tasks. By left clicking and selecting External Links the user is taken to a webservice with information about the selected taxon. This a user configurable system which now point to ALA, APNI, APII and EOL but a clever user can configure the viewer to go anywhere.





Figure 4. Move around screen with the arrows, expand or contract tree or click and drag to move around screen.



Figure 5. When hovering over a terminal the character states appear.



Figure 6. Options appear when left clicking on a terminal or node.



Figure 7. These options appear when External Links is clicked.

Tabs

There are seven tabs which allows the user navigate and configure the tree. Users can change the view scale, collapse or expand select clades, reroot the tree. In any web browser, viewers can change the presentation of the tree. They can swap the order individual paired branches or sort the whole tree by branch length (ladderize). They can search the tree for a taxon name – corresponding to a subtree or terminal taxon. The options tab controls tree viewing options such as expanding/contracting nodes. It is often helpful for viewing character information to check the align names box. This displays all symbols in columns for easier comparisons. The character tab allows selection of characters, up to ten at a time, to be mapped on the tree. Note that the tree branches are colored based on the characters states, and ancestral state reconstructions, of the first character selected.

The Legend tab provides a legend of the character states for all chosen characters. Quantitative character states are divided into 10 section of equal size and blue heat map is used to color the 10 character states. Qualitative characters are coded with symbols and colors to differentiate character states. PhyloJIVE does allow the input of multiple character states however multiple characters states do not reconstruct on the tree. If a terminal has two character states a new colored symbol is produced which is called multiple. The individual character states are identified on the tree by terminal taxon. The Map tab will show the distribution map of a selected terminal or nodes. The default is to color the map by terminal name (species), that is each terminal is indicated with a different color. The user has the option of selecting one of the characters to display on the map. For example the A node with ten terminals can be selected and the default will be a map with ten colors one for each species. Alternatively the user can use the colour by toggle box and select habit. Now the map will be colored by the character state tree or shrub. The trait values come for the coding of the species for that trait. Double clicking on the map will produce a larger map for easier viewing. The Search tab allows the use to search for a terminal taxon. The taxon will be highlighted if found but the use will have to navigate to the terminal branch.

F

igure 8. The right panel has several tabs. These allow the user to select characters to map, view legend, search for a terminal name and see a distribution map.​

Character Tab

Viewers may select up to ten characters for simultaneous display on the tree. These data can with be from the users upload function of the Input tab or pulled from pre-configured webservices. The Character tab allows selection of the character from a pull down menu that combines the user uploaded and the webservices derived data. The data can be a mix of qualitative or quantitative data. Character 1 is used to color the branches of the phylogenetic tree. When hovering the mouse over a terminal or node the character state is given in a floating box. The data at the nodes is from an ancestral state reconstruction (see below). In order to give the viewers a quick overall impression of the distribution of character states for multiple characters colored symbols are used to display the data along with the actual value that is available while hovering over the node or terminal. Quantitative characters are shown by a heat map while qualitative characters are mapped with a colored symbol. Putative differences in the ancestral states qualitative characters are inferred from (Fitch) parsimony. Putative changes in the ancestral states of quantitative characters are inferred from a phylogenetically weighted comparison of means and standard deviations. The reconstructed ancestral state of the first character is used to determine branch colour. Transitions in any of the three selected characters is indicated by a red box.





Figure 9 & 10. Users can map morphological characters on the phylogeny, if characters are available as a .csv file or from a linked webservice such as Identify Life. Left, up to 10 characters can be selected and mapped at one time in the characters tab and the character state legend is available in the Legend tab, right.

Maps

Distribution maps of the terminal are available another new feature is the ability to view a map of occurrence records for a given taxon or ancestral node. These data are available through the external links outlined above or can be directly mapped in the Map tab. Currently PhyloJIVE is configured to generate the maps by accessing the point data from the Atlas of Living Australia. This can be configured by the viewer to generate maps of non-Australian taxa by accessing the data from any other webservice. The viewer can left click on a terminal and select View Map and the distribution map will appear in the Map tab. Distribution maps for multiple taxa (up to 32) can also be accessed at nodes by left clicking on the node and selecting View Map. The default value is to colour dots by species thereby simultaneously mapping multiple taxa each with a different colour. The user has the option, in the Map tab, “Colour By: pull down menu to colour the map by any character. For example the user could select a node and map by species and then select the character habit and see the geographic distribution of trees versus shrubs for that node. Lastly, these maps can be the basis of a spatial analysis by automatically importing the different colour schemes as separate spatial layers in the ALA spatial portal. Clicking the link “View in Spatial Portal” opens the ALA Spatial Portal in a new window (shown below). Layers can be hidden, combined, filtered by other criteria (e.g. collector, institution, etc) and various environmental layers can be overlaid or used as the basis of modelling, etc.



 

Figure 11 & 12. Distribution maps accessed by left clicking over a node or terminal and selecting view map of single terminals (left) and up to 32 members of a clade (right). Current source of the map points is the Atlas of Living Australia but this is configurable.

How to upload your data

Users can upload their own phylogenetic tree and character dataset into the ALA version of PhyloJIVE. At present this will access the character mapping and reconstruction functions. If the taxon is Australian it will map and also access the nomenclature.

To upload data first the user must join the ALA user list. After login a line of text will appear above the tree viewing box indicating access to Create a New Tree. Select Tree List, in this window the use can select to view a number of publically viewable trees and datasets in PhyloJIVE. To upload you own tree the user selects New Phylogenetic Tree. The user fills in the needed information and uploads a Newick tree and a .csv file with morphological data. It is best to simply copy and paste the text files in the correct boxes. Do not leave extra spaces or returns at the end of the files. It is critical the terminal names on the tree are identical to the csv file. The csv file should be first column terminal names and starting with the second column header being the character with character states following for the taxa. Full and correct binomials are necessary to connect to the external links. Please see the attached example files.

Sample datasets: Acacia phylogeny:

Miller, J.T., D. M. Murphy, G. K. Brown, D. M. Richardson and C. E. González-Orozco. 2011. The evolution and phylogenetic placement of invasive Acacia species Diversity and Distributions. 17:848-860.



((((((((((((Acacia deanei:0.029395999999999978,Acacia mearnsii:0.04198500000000005,Acacia mearnsii:0.009386000000000005):0.025534000000000057,Acacia muelleriana:0.05095799999999995):0.009724999999999984,(Acacia dealbata:0.013597999999999999,Acacia dealbata:0.04765799999999998):0.06518100000000004,(Acacia linifolia:0.053427,Acacia spectabilis:0.07935999999999999):0.03228399999999998):0.011299999999999977,Acacia dorothea:0.04428500000000002):0.025370000000000004,(Acacia penninervis:0.010780000000000012,Acacia penninervis:0.013546999999999976):0.027490000000000014):0.022839000000000054,((Acacia cultriformis:0.051591000000000053,Acacia falcata:0.067639):0.036248999999999976,(Acacia neriifolia:0.05405700000000002,Acacia pravissima:0.08901599999999998):0.035804999999999976):0.01113900000000001):0.08552600000000005,((((Acacia amblyophylla:0.191411,Acacia meissneri:0.036506999999999956):0.023009000000000057,Acacia anceps:0.09021299999999999):0.034943999999999975,Acacia euthycarpa:0.067473):0.009916000000000036,(Acacia beckleri:0.07366899999999998,Acacia pycnantha:0.07797299999999996):0.03950200000000004,(Acacia hakeoides:0.06449499999999997,Acacia hakeoides:0.05915199999999998):0.04348099999999999):0.024106000000000016):0.14326599999999995,((((((Acacia aneura:0.06850299999999998,Acacia aneura:0.185102):0.11921999999999999,(Acacia gonoclada:0.13806600000000002,Acacia holosericea:0.09942899999999999):0.047653999999999974):0.023492999999999986,(Acacia abbreviata:0.175033,Acacia crassicarpa:0.10139299999999996):0.06082900000000002):0.032843999999999984,Acacia multispicata:0.147733):0.05070999999999992,(Acacia floribunda:0.15847300000000003,Acacia triptera:0.13394199999999995):0.02024699999999996):0.046435000000000004,(((Acacia cognata:0.298748,Acacia flexifolia:0.06810700000000003):0.039027000000000034,(Acacia venulosa:0.10495200000000005,Acacia viscidula:0.12380199999999997):0.03825400000000001):0.01595599999999997,(Acacia baeuerlenii:0.14029000000000003,Acacia melanoxylon:0.16516799999999998):0.04455399999999998):0.11580999999999997):0.04352299999999998):0.12480200000000008,(((Acacia murrayana:0.271116,Acacia pachyacra:0.08749700000000005):0.09907100000000002,Acacia subrigida:0.33091000000000004):0.17799300000000007,(Acacia suaveolens:0.595355,Acacia triquetra:0.349507):0.06649000000000005):0.06937499999999996):0.04425599999999996,(((((((Acacia leioderma:0.09380500000000003,Acacia pentadenia:0.09877999999999998):0.218746,(Acacia hemiteles:0.08961200000000002,Acacia guinetii:0.11649100000000001):0.20321999999999996):0.11906499999999998,(Acacia adoxa:0.05807399999999996,Acacia perryi:0.06811599999999995):0.2606519999999999):0.03101300000000007,Acacia pravifolia:0.27304800000000007):0.03586199999999995,((Acacia cupularis:0.039309999999999956,Acacia ligulata:0.02492300000000003):0.19357899999999995,Acacia rostellifera:0.245108):0.22407599999999994):0.048131000000000035,Acacia extensa:0.28929799999999994):0.02978499999999995,((Acacia saligna:0.10582400000000003,Acacia saligna:0.06461700000000004):0.21633999999999998,Acacia alata:0.35306400000000004):0.08363799999999999):0.06725000000000003):0.03506100000000001,((Acacia dempsteri:0.187512,Acacia pyrifolia:0.12982800000000005):0.08194299999999999,Acacia victoriae:0.42759500000000006):0.21501400000000004):0.0698625,(Pararchidendron pruinosum:0.247707,Paraserianthes lophantha:0.646114):0.0698625);

Sample datasets: Trait data: csv file

species,invasiveness,fake_data_1,fake_data_2,fake_data_3,fake_data_4,fake_data_5

Acacia abbreviata,not invasive,tall,yellow,1,100,1265

Acacia acuminata,not invasive,tall,yellow,1,100,1265

Acacia adoxa,not invasive,tall,yellow,1,100,1265

Acacia adunca,not invasive,tall,yellow,1,100,1265

Acacia alata,not invasive,tall,yellow,1,100,1265

Acacia anceps,not invasive,tall,yellow,1,100,1265

Acacia aneura,not invasive,tall,yellow,1,100,5656

Acacia argyrophylla,not invasive,tall,yellow,3,100,5656

Acacia aspera,not invasive,tall,yellow,3,100,5656

Acacia aulacocarpa,not invasive,tall,yellow,3,100,5656

Acacia auriculiformis,not invasive,tall,yellow,3,600,5656

Acacia baeuerlenii,not invasive,tall,yellow,3,600,5656

Acacia baileyana,invasive,tall,yellow,3,600,5656

Acacia beckleri,not invasive,tall,yellow,3,600,5656

Acacia binervata,not invasive,tall,yellow,3,600,5656

Acacia brachystachya,not invasive,tall,yellow,3,600,5656

Acacia calamifolia,not invasive,tall,yellow,3,600,5656

Acacia calcicola,not invasive,tall,yellow,3,600,5656

Acacia cardiophylla,not invasive,tall,yellow,7,600,5656

Acacia cognata,not invasive,tall,yellow,7,600,5656

Acacia confluens,not invasive,tall,yellow,7,600,5656

Acacia crassicarpa,invasive,tall,yellow,7,600,5656

Acacia cultriformis,not invasive,tall,yellow,7,600,5656

Acacia cupularis,not invasive,tall,yellow,7,600,5656

Acacia cyclops,invasive,tall,yellow,7,600,5656

Acacia dealbata,invasive,tall,yellow,7,600,5656

Acacia deanei,not invasive,tall,yellow,7,600,5656

Acacia decurrens,invasive,tall,yellow,7,600,5656

Acacia dempsteri,not invasive,tall,yellow,7,600,5656

Acacia doratoxylon,not invasive,tall,yellow,7,600,5656

Acacia dorothea,not invasive,tall,yellow,7,600,5656

Acacia elata,not invasive,tall,red,7,600,5656

Acacia elongata,not invasive,tall,red,7,600,5656

Acacia epacantha,not invasive,tall,red,7,600,5656

Acacia euthycarpa,not invasive,tall,red,7,600,5656

Acacia extensa,not invasive,tall,red,7,600,4236

Acacia falcata,not invasive,tall,red,6,600,4236

Acacia fimbriata,not invasive,tall,red,6,600,4236

Acacia flexifolia,not invasive,tall,red,6,600,4236

Acacia floribunda,not invasive,tall,red,6,600,4236

Acacia genistifolia,not invasive,tall,red,6,600,4236

Acacia gonoclada,not invasive,tall,red,6,225,4236

Acacia guinetii,not invasive,tall,red,6,225,4236

Acacia hakeoides,not invasive,tall,red,6,225,4236

Acacia hammondii,not invasive,short,red,6,225,4236

Acacia hemiteles,not invasive,short,red,6,225,4236

Acacia heteroclita,not invasive,short,red,6,225,4236

Acacia holosericea,invasive,short,red,6,225,4236

Acacia howittii,not invasive,short,red,6,225,4236

Acacia implexa,invasive,short,red,6,225,4236

Acacia irrorata,not invasive,short,red,2,225,4236

Acacia ixiophylla,not invasive,short,red,2,225,4236

Acacia jonesii,not invasive,short,red,2,225,4236

Acacia kempeana,not invasive,short,red,2,225,4236

Acacia lasiocalyx,not invasive,short,red,2,225,4236

Acacia leioderma,not invasive,short,red,2,225,4236

Acacia ligulata,not invasive,short,red,2,225,4236

Acacia lineata,not invasive,short,red,2,225,4236

Acacia linifolia,not invasive,short,red,2,225,4236

Acacia longifolia,invasive,short,red,2,225,4236

Acacia longissima,not invasive,short,red,2,225,4236

Acacia mearnsii,invasive,short,red,2,225,4236

Acacia meisneri,not invasive,short,red,2,225,4236

Acacia melanoxylon,invasive,short,red,4,225,4236

Acacia montana,not invasive,short,red,4,225,8453

Acacia mucronata,not invasive,short,red,4,225,8453

Acacia muelleriana,not invasive,short,red,4,225,8453

Acacia multispicata,not invasive,short,red,4,225,8453

Acacia murrayana,not invasive,short,red,4,225,8453

Acacia neriifolia,not invasive,short,red,4,225,8453

Acacia oswaldii,not invasive,short,red,4,225,8453

Acacia pachyacra,not invasive,short,red,4,225,8453

Acacia parvipinnula,not invasive,short,red,4,225,8453

Acacia penninervis,not invasive,short,red,9,777,8453

Acacia pentadenia,not invasive,short,yellow,9,555,8453

Acacia perryi,not invasive,short,yellow,9,555,8453

Acacia podalyriifolia,invasive,short,yellow,9,555,8453

Acacia pravifolia,not invasive,short,yellow,9,555,8453

Acacia pravissima,not invasive,short,yellow,9,555,8453

Acacia prominens,not invasive,short,yellow,9,555,8453

Acacia pruinosa,not invasive,short,yellow,9,555,9826

Acacia pubescens,not invasive,short,yellow,9,555,9826

Acacia pycnantha,invasive,short,yellow,9,555,9826

Acacia pyrifolia,not invasive,short,yellow,9,555,9826

Acacia ramulosa,not invasive,short,yellow,9,555,9826

Acacia retinodes,not invasive,short,yellow,9,555,9826

Acacia rigens,not invasive,short,yellow,9,555,9826

Acacia rostellifera,not invasive,short,yellow,9,555,9826

Acacia saliciformis,not invasive,short,yellow,9,555,9826

Acacia saligna,invasive,short,yellow,9,555,9826

Acacia schinoides,not invasive,short,yellow,9,555,9826

Acacia silvestris,not invasive,short,yellow,9,555,9826

Acacia spectabilis,not invasive,short,yellow,2,555,9826

Acacia stenophylla,not invasive,short,yellow,2,555,9826

Acacia stigmatophylla,not invasive,short,yellow,2,555,9826

Acacia suaveolens,not invasive,short,yellow,2,555,4761

Acacia subrigida,not invasive,short,yellow,2,555,4761

Acacia subulata,not invasive,short,yellow,2,555,4761

Acacia triptera,not invasive,short,yellow,2,555,4761

Acacia triquetra,not invasive,short,yellow,2,555,4761

Acacia venulosa,not invasive,short,yellow,2,555,4761

Acacia verniciflua,not invasive,short,yellow,2,555,4761

Acacia verticillata,invasive,short,yellow,2,555,4761

Acacia vestita,not invasive,short,yellow,2,777,4761

Acacia victoriae,invasive,short,yellow,2,777,4761

Acacia viscidula,not invasive,short,yellow,2,777,4761

Acacia wattsiana,not invasive,short,yellow,2,777,4761

Pararchidendron pruinosum,not invasive,short,yellow,2,777,4761

Paraserianthes lophantha,invasive,short,yellow,2,777,4761

Acacia amblyophylla,not invasive,short,yellow,2,777,4761

Acacia meissneri,not invasive,short,yellow,2,777,4761

Additional information including screencasts is available at: http://www.acaciamulga.net/#!about1/cdyi



1 http://phylojive.ala.org.au/treeViewer/show/Case+Study+II%3A+marsupials+-+species+level



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