COMING SOON: New Phylogenetic ‘Tree of Life’ Tools

COMING SOON: New Phylogenetic ‘Tree of Life’ Tools

The Atlas of Living Australia (ALA), in collaboration with the creators of PhyloJIVE, will soon be introducing new tools to explore species data and relationships from a phylogenetic (or tree of life) perspective. The tools are intended for both novices and experts alike, and aim to make phylogenetic approaches to data exploration and visualisation accessible to a broad range of audiences.

A phylogenetic tree showing the evolutionary relationships between Acacia species (left) is intersected with ALA Acacia records and precipitation layers to reveal the rainfall envelope occupied by a clade of Acacias. The envelope occupied at present (top right) can be compared to the envelope that would be occupied under 2030 predicted rainfall (bottom right).

 

A phylogeny (or a tree of life) is essentially a theory about how organisms are related to one another through evolutionary time. Phylogenies are based on the assumption that more closely related species will be more similar to one another, and they are commonly built using genetic sequences or physical characters. They are often visually represented as trees: the tips of the ever branching tree representing species, and the branches representing ‘evolutionary distance’ (e.g. length of time) from the ancestors from which they evolved.

 

ALA’s new phylogenetic tools integrate phylogenetic trees and spatial mapping so that phylogenies can be represented spatially by, for example species occurrence or character. Here, the occurrence of Acacia species from the clade highlighted by the green node is mapped and coloured by species.

 

The new ALA-PhyloJIVE tools intersect species occurrence data with environmental layers and phylogenetic trees, enabling a variety of new perspectives on biodiversity. For example, you will be able to investigate the environmental envelopes occupied by the species of any chosen clade (a group of related organisms sharing a common ancestral node). You can also measure and compare biodiversity for any given area/s in ways that account for both the number of species occurring there, and their evolutionary distinctness from one another, using phylogenetic diversity. The tools will also allow you to map the spatial distribution of characters (e.g. waxy leaves) across the landscape.

 

Phylogenetic Diversity (PD) of amphibians (grid cells 50x50km) with darker areas indicating higher PD. With ALA’s new tools PD can be assessed at a continental scale (as shown here), or compared between any number of user-defined areas, providing new options for exploring biodiversity patterns. (Map not corrected for patchy sampling. Source tree: Pyron RA, Wiens JJ. 2011. A large-scale phylogeny of Amphibia with over 2,800 species, and a revised classification of extant frogs, salamanders, and caecilians. Molecular Phylogenetics and Evolution 61: 543-583.)

 

Watch this space for notification of the availability of these phylogenetic tools. Your feedback on the tools will be welcome.

For more information, please contact support@ala.org.au.

A Case Study

Simon Connor
School of Earth, Atmosphere and Environment, Monash University 

This case study describes a practical exercise developed for students in the School of Geography and Environmental Science at Monash University.  The exercise is based around simple bioclimatic modelling techniques and designed for first-year university students of biogeography, ecology and climatology.  It incorporates aspects of past, present and future climates and their impact on species distributions, particularly in Victoria, but could be easily modified to suit any part of Australia.

Context

Climate change is one of the biggest issues facing Australia’s biodiversity.  Some of the country’s ecosystems are considered to be particularly vulnerable to increased temperatures and changing rainfall patterns (Laurance et al., 2011) and our species may have to migrate long distances across fragmented landscapes in order to survive (Hughes, 2014).  Knowing what will happen to various species and ecosystems is vital to ensuring that conservation and management efforts are applied where they are most needed.

It is also important to increase public awareness of current threats to Australia’s unique biodiversity.  A public understanding of the methods scientists use to predict biodiversity changes into the future is a responsibility of scientists.  Too often scientific research remains hidden in journals accessible only to academics.  Universities have enormous opportunities to influence public engagement in science through their education programmes.  This exercise aimed at helping students to create their own bioclimatic models may also give the public insights into how scientists are grappling with the future of Australia’s biodiversity.

The exercise

The practical exercise has three main parts: the first is on animal distributions under current and future climates; the second concerns plant distributions in the past and present; and the third part looks at how rare and endangered species may respond to future climate change in alpine environments.

The first part focuses on the brushtail possum (Trichosurus vulpecula) and the ringtail possum (Pseudocheirus peregrinus), which are common marsupials in Melbourne backyards and familiar to most students.  We use the Atlas of Living Australia (ALA) to examine the possums’ distributions in Australia and compare them to maps of annual mean temperature and annual rainfall (two basic climatic variables, though not necessarily the most important for possum distributions!)  Possum distributions are then projected into climate space using the Scatterplot function in the ALA and the students identify the core range of each species.  They then modify the temperature and rainfall of Melbourne, Adelaide and Sydney according to climate predictions for 2070 to see whether any of these cities will fall outside the core range of the two possum species by 2070.  The students are then asked to use their predictions to decide where to prioritise possum conservation efforts among the three cities.

The second part concerns the Southern Beech (Nothofagus cunninhamii), a long-lived, late-successional tree found in cool-temperate rainforests in southern Australia.  We give the students some basic ecological information about this species, along with distribution maps and a table with selected bioclimatic variables for its current range.  Students compare the current bioclimate of Nothofagus cunninghamii with that of Buxton, an area where the species apparently went extinct around 6,000 years ago (McKenzie & Busby, 1992).  They also compare the current bioclimate to that of Falls Creek, a well-known ski village on the Bogong High Plains.  Based on their observations, the students come up with an explanation for the local extinction of beech at Buxton and the reasons why it does not currently live at Falls Creek.  This part of the exercise emphasises the potentially important role of palaeoecological data in reconstructing the climates of the past, and also highlights the importance of ecological factors such as dispersal rates and fire sensitivity.  The lecture that accompanies the practical exercise also raises the possibility that the intensification of the El Niño Southern Oscillation (ENSO) during the mid-Holocene may have impacted the species.

The final part of the practical exercise relates to two rare or endangered species on the Bogong High Plains: a plant, the Bogong Eyebright (Euphrasia eichleri), and a mammal, the Mountain Pygmy Possum (Burramys parvus).  The Bogong High Plains are part of the Australian Alps and include Victoria’s highest peak, Mt Bogong (1986 m).  The ALA’s Predict function is employed to create niche models for the two species based on the “best 5 independent terrestrial layers”.  Although these layers may not necessarily be the most appropriate for the two species in question, it is an easy introduction for students before experimenting with the 400+ layers available through the ALA (see discussion in Williams et al., 2012).  Environmental lapse rates are then introduced and used to predict how a 3 °C temperature rise might impact on species distributions.  The students map the current and future ranges of the two species to translate their altitude-based predictions back into geographical space.  Finally, the exercise congratulates the next generation of bioclimatic modellers for their efforts and encourages them to think more broadly about non-climatic factors that could be critical to the management of rare and endangered species.

Review

This exercise was introduced to first-year physical geography classes at Monash in 2013 and was well received by students and their demonstrators.  Although the practical class could not be held in a dedicated computer lab, students appreciated the option to use their own computer and experiment with the ALA during class time.  A handful of students completed the exercise in less than an hour; the remainder completed it within the two hours allocated.  There was also a strong link between the lecture material and the practical class, so the relevance of the exercise to the lectures was clear.  Most students clearly understood the importance of what they were doing and gained an appreciation of the potentials and pitfalls of bioclimatic modelling.  This was reflected in high levels of engagement and high marks for the exercise.  On completing the map on the final page of the exercise, one student declared, “Well, I guess that plant is stuffed!”  Using the publicly available ALA data and tools empowers students to make their own scientifically informed decisions about biodiversity issues in Australia and encourages independent exploration and experimentation.  Despite the simplicity of the practical exercise’s approach to bioclimatic modelling, it lays the groundwork for more sophisticated modelling if students decide to pursue this in later years.

The ALA proved to be an excellent educational tool in this context.  Its unique combination of user-friendly interface and powerful modelling capabilities makes it far more amenable to student work than any available alternative.  It is difficult to imagine any other application that allows students to create professional-standard distribution maps, bioclimatic scatterplots and niche models so simply, quickly and intuitively.  The inclusion of species photo galleries and the possibility of contributing to citizen science data were also attractive to students.  Minor drawbacks include the presence of fossil data in the ALA. Such records may be difficult to detect without examining records individually. There are also some noticeable data gaps where agencies have not provided information to the ALA (e.g. brushtail possum records from the Department of Environment and Primary Industry, Victoria – but these records along with many others are in the process of being added).

It is hoped that others will adapt this practical exercise and report back to the ALA with new exercises, improvements, suggestions and tips.  The ALA is a tremendous educational resource, so let’s all start talking about how best to use it.  The possibilities are only limited by our imagination!

References

Hughes, L. (2014) Changes to Australian terrestrial biodiversity. In: Christoff, P. (ed.) Four Degrees of Global Warming: Australia in a Hot World. Routledge, Oxon (UK), pp. 63-83.

Laurance, W.F., Dell, B., Turton, S.M., Lawes, M.J., Hutley, L.B., McCallum, H., Dale, P., Bird, M., Hardy, G., Prideaux, G., Gawne, B., McMahon, C.R., Yu, R., Hero, J.-M., Schwarzkopf, L., Krockenberger, A., Douglas, M., Silvester, E., Mahony, M., Vella, K., Saikia, U., Wahren, C.-H., Xu, Z., Smith, B. and Cocklin, C. (2011) The 10 Australian ecosystems most vulnerable to tipping points. Biological Conservation 144: 1472–1480.

McKenzie, G.M. and Busby, J.R. (1992). A quantitative estimate of Holocene climate using a bioclimatic profile of Nothofagus cunninghamii (Hook) Oerst. Journal of Biogeography, 19: 531-540.

Williams K.J., Belbin L., Austin, M.P., Stein, J. and Ferrier, S. (2012).  Which environmental variables should I use in my biodiversity model? International Journal of Geographic Information Sciences 26: 2009-2047. http://www.tandfonline.com/doi/pdf/10.1080/13658816.2012.698015

By Linda Riquelme.

Since its inception in 2006, the Atlas of Living Australia has become the most comprehensive public access point for information about all living things on land and in water in the Australian region. While there are areas that may be lacking data, the Atlas team is constantly working with data providers to obtain more data. And, of course, your help in filling the gaps in the Atlas would be greatly appreciated!

I have had the privilege of spending my summer with the team at the Atlas of Living Australia at CSIRO in Canberra. As the work experience person, I am responsible for the coffee runs.

Just joking!

My main priority has been to work with Lee Belbin to create layouts for more comprehensive area reports. The Area Report tool (Tools | Area Report) is an invaluable part of the Spatial Portal, allowing users to obtain a summary of biologically-related data in a specific area.

Current on-screen area report

Figure 1. Current on-screen area report

For example, a park manager can use the area report to quickly and easily get an idea of all the data available for a particular national park. By going into the Spatial Portal, they can select the national park from the Collaborative Australian Protected Areas Database (CAPAD) layer, and then generate an area report.

Currently, when an area report is generated, you are provided with information on area size, the number of species (including iconic, endemic and pest species), as well as other information like expert distributions (fig. 1).

Area reports can be used for research, park management, natural resource and catchment management, consulting (e.g. environmental impact assessments), and farm, local and state/territory government planning. Area reports also provide an opportunity to discover more about Australia’s biodiversity.
Information that we plan to add to the on-screen area report will include:
Dynamic land cover classes (terrestrial)

  • IMCRA bioregions (marine)
  • Species lists by lifeform
  • Specimens with DNA sequences
  • Migratory species lists
  • Threatened species lists and classifications

In addition to the on-screen area report, a comprehensive area report in PDF format will be developed. This will collate everything that is known about an area into a single, downloadable PDF-formatted report. Features that will be included in the PDF report that won’t appear on the on-screen report include:

  • Global context ecoregions: Terrestrial/Marine/Freshwater Ecoregions of the World (TEOW/MEOW/FEOW)
  • Sensitive species lists
  • Classification of area maps (fig.)
  • Net Primary Productivity (NPP) maps (fig.)
Classification of Area

Figure 2a. Classification of area

Net Primary Productivity

Figure 2b. Net primary productivity

The Atlas of Living Australia has just reached 1 billion downloads (and counting). With the enhanced area report, the Atlas of Living Australia can continue to provide biological and environmental information to assist in research, monitoring and the decision-making processes. The future of biodiversity information sharing looks bright!

Ben Raymond, scienceuntangled.com and R.O. (Bob) Makinson, Royal Botanic Gardens & Domain Trust

Scientific analyses are usually driven by a research question: frame the question and then collect or find the data that will allow it to be answered. Sometimes, though, it can be useful to work in the other direction: given data, find some questions to answer. The Atlas of Living Australia provides a wealth of biodiversity data, including occurrences, species profiles, taxonomic and name information, and photographs. This diversity of data, readily accessible through the ALA’s open web services, provides a foundation for analyses and visualizations that otherwise would be much more difficult, and perhaps might not even be considered.

Grevilleas are members of the Proteaceae plant family (which also includes proteas, waratahs, and banksias) and are widespread across Australia. They are evergreen shrubs or trees with a diverse range of flower and leaf shapes. The aim of this analysis was to visualize the spatial variation in Grevillea flower colour across Australia. This was done by first extracting species-specific flower colour information from photographs, and then linking this information to the locations of observations of those species.

Photograph processing

Species lists (taxon name and occurrence count) were extracted in each 1-degree square across Australia, using the Atlas of Living Australia’s occurrences web service (see http://biocache.ala.org.au/ws/). The ALA profile page for each species was also retrieved (e.g. Grevillea baxteri). These profile pages generally include a pointer to a photograph, which was downloaded and saved where available. Photographs were also retrieved from NSW Flora Online and the Australian National Botanic Gardens. The photograph that best depicted the flowers of a given species was chosen from those available.

The flowers (usually aggregated, in a conflorescence) in each photograph were manually delineated, and their colours tabulated. Some example photographs and their corresponding colour palettes are shown below.

Grevillea aneura

Grevillea barklyana

Grevillea tenuiloba

Spatial reconstruction

The colour palettes were then linked back to the species lists in the 1-degree grid squares. A sample of colours in each grid cell was taken, keeping the relative proportion of colours true to the colour distribution within each species palette.

The resultant map is shown below. Grey indicates areas where Grevillea occurrence records were lacking, incomplete, or were for other reasons not used in the present analyses. Broad patterns in colour are apparent, with red colours most dominant in the southern parts of the continent.

Red- and orange-flowered species are typically pollinated by birds; yellow- and cream-coloured ones by insects, although there are exceptions to these general trends. This general latitudinal trend in Grevillea flower colour has been recognized by botanists for some time, although not formally published to our knowledge. However, it is worth noting that these analyses were entirely data-driven, and were not based on this existing knowledge.

Grevillea colour

Limitations

The sources of information used in this analysis were not exhaustive. Photographs were not available for all Grevillea species, and some were not suitable for extracting flower colours. The available photographs were also quite varied in terms of their resolution, lighting, and subject (with some specifically detailing the flowers; others the plant more generally). Survey effort, and therefore occurrence information, is also highly variable across Australia, particularly in remote areas. Additional occurrence data and imagery, for example from State herbaria and non-government sources, could provide a more comprehensive and detailed information base from which to work.

Future directions

For this initial run, palettes were based on overall flower/conflorescence colours. The colours of the styles and perianth were not differentiated. These within-flower contrasts may be important for pollinators, and may show their own spatial distribution patterns. The aggregation of palettes for multiple species within grid squares, and the non-differentiation of subgeneric groups (which sometimes correlate with insect- vs bird-pollination syndromes) may mask trends that remain available to more targeted future analyses.

Trends in the geographical patterning of flower colour could also be assessed and compared on the basis of subgeneric groupings within Grevillea. A full phylogeny of the genus is not yet available (but is in progress); in the meantime there are generally accepted morphologically-based groupings of species (Makinson, 2000). These include many potentially informative vicariant sister-sets (tropical/eremaean, tropical/temperate, western temperate/eastern temperate). The close sister genus Hakea, although not as speciose, is similarly widely distributed and also contains several infrageneric groups. Eventual analysis using both genera and their sub-groups, overlaid with known or inferred pollination syndromes, would improve resolution of spatial colour trends, allow significance testing by correlation, and allow some correction for over-dominance of some highly speciose and better known species-groups.

Trends in this tribe of Proteacece could then be assessed in relation to those in other plant families considered to be comparable in terms of distribution, colour variation, and quasi-correlated pollination modes. The tribe Melaleuceae (sensu Wilson et al. 2005) in the family Myrtaceae is one likely candidate.

The delineation of flowers within photographs was done manually in this instance and was a somewhat time-consuming process. Initial experiments with automated methods have shown promise, and are being developed further.

References

Makinson RO (2000) Proteaceae 2: Grevillea. Flora of Australia vol. 17A. ABRS, Canberra / CSIRO Publishing, Melbourne.

Wilson PG, O’Brien MM, Heslewood MM, Quinn CJ (2005) Relationships within Myrtaceae sensu lato based on a matK phylogeny. Plant Systematics and Evolution 251:3–19.

Due to demand – I have produced a detailed user manual for the Atlas of Living Australia’s Spatial Portal (SP).  This is intended to be a stand-alone document that provides the context for, and philosophy behind the SP as well as a deeper insight into its many tools.  The manual covers all aspects of the SP with advice, examples and references.  I’m very grateful to Margaret Cawsey, John Tann and John Busby for providing extensive feedback and suggestions. I hope that all of their comments have been incorporated.

Koppen climate classification

Koppen climate classification

In putting together this document, an issue we all face is that the SP and other Atlas tools are constantly responding to user feedback and improving through the work of a talented programming team.  As such, this document will become out of date over time but we will update the manual as often as possible after system updates.

Some items that we are looking forward to work on include:

  1. Greatly extending the current Area Report – to integrate a far wider range of bio-environmental information within the Atlas.   Comprehensive bio-oriented reports on any defined area will be of great use for local Government, environmental impacts assessments, land owners, land managers, research etc. As ever, ‘area’ in the SP can be defined in any of 14 different ways.
  2. Develop a library of scripts, leveraging existing Atlas web services, to enable users of the R package to access Atlas data.  This is in response to feedback from researchers that efficient access to Atlas data via R will be highly valuable.  This work will also improve the web services themselves and deliver some updated documentation on how to use these services.  We are still considering integrating more analysis tools within the portal itself but this work with the R software will immediately support a wide range of analyses.
  3. Improve our approach to data on invasives, aliens, pests etc – such that they parallel how we currently handle conservation status. This domain is of immense cost/value to Australia so it is vital that we present a useful and consistent interface to relevant information that can be used for the broadest applications.  This includes the ability to answer questions such as: what invasives exist in a given area - and, by further leveraging our lists tool we will soon be making this information available in the extended Area Report as mentioned above.
  4. Continue outreach to the scientific community.
    1. I visited Professor Steven Chown and Associate Professor Melodie McGeoch at Monash in September and it was gratifying to see how the Atlas is being used in teaching and research at Monash. We are looking to ways that the Atlas can better assist in this environment.
    2. A presentation on ‘Data Quality’ has been accepted for ESA2013. This continues to be a hot topic, and one that the Atlas continues to work on.
    3. We hope to have a resource available in the near future to help with the delivery of targeted resources for education and training purposes.
  5. In general, we continue to review and manage the spatial layers in the Spatial Portal as resources allow – so do do let us know if there are particular layers and climate models/scenarios that you would like to have incorporated.  Note that we have recently included the Koppen climate classification  (see image above).

Feedback on any of these items would be valued.

Lee Belbin

Author: 

Here in Australia we have a wide range of fantastic continental scale systems for monitoring elements of our environment, from the climate, atmosphere, water and oceans, to earthquakes and tremors, and vegetation and land cover.

Bureau of Meteorology weather monitoring systems, such as their rainfall radar, aid decision-making – like knowing when it’s safe to take your hairdo outside.

Historically, these environmental domains have been well served. Most people would be familiar with the Bureau of Meteorology’s (BoM) weather and climate monitoring, for example.

(Their rainfall radars have saved my hairdo on more than one occasion)

Operated by the likes of BoM and Geoscience Australia, environmental monitoring systems have allowed the Australian Government to make informed continental-scale decisions, and they are also put to good use by countless others, not least our maritime, aviation and agriculture industries.

What we haven’t had on a continental scale though is consistent information about Australian biodiversity that can support national decision-making. There has been no system in place that spans the continent and can tell us how the diversity of species is changing over time and over geographic space.

To address this deficit, a collaboration of BoM, CSIRO and the Atlas of Living Australia have looked into how such a system might work and released their findings in a new report‑Biodiversity Profiling: Components of a continental biodiversity information capability.

Importantly, they found that it would be possible to put a biodiversity assessment system in place using existing capability, such as data stores, environmental modelling tools and spatial information.

The team found that the Atlas of Living Australia, an online database of Australian biodiversity that has brought information from our natural history collections, state and territory conservation agencies, biodiversity interest groups and individuals, together with related environmental and mapping data, provides a unique opportunity to establish a continental-scale biodiversity assessment system.

An applied case study in the report shows that data contained within the Atlas can be combined with environmental data to derive models of biodiversity patterns, which can then be combined with satellite imagery, such as that acquired by the National Carbon Accounting System, to infer patterns of biodiversity loss or retention in individual regions. The authors say this demonstrates the potential for data and models to be linked for continent-wide monitoring.

Further development of the Atlas and the Terrestrial Ecosystem Research Network, which champion consistent ecological research, monitoring and data sharing across the continent, are rapidly improving our nation’s ability to monitor the landscape.

By integrating data collection and modelling capabilities with the monitoring systems of BoM, Geoscience Australia and other government agencies, there will be new opportunities to understand ecological change and support the Australian Government’s continental-scale decision-making.

Download the full report

An indication of the spatial data held by the Atlas of Living Australia. This map is a snapshot in time showing the occurrence density of biological records on the Atlas.

This article first appeared on the CSIRO News Blog (2013/09/19)

By Andrea Wild

From ugly ducklings like the Rough Dreamer to the kiss-me-I’m-really-a-prince Clown Triggerfish, Australia’s marine fishes are now at your fingertips thanks to FishMap, officially launched on Tuesday 26 February, 2013, by the Atlas of Living Australia .

Rough Dreamer

FishMap is a free online mapping tool that anyone can use to find out which fishes occur at any location or depth in the waters of Australia’s continental shelf and slope. You can create species lists for any region that include photographs and illustrations, distribution maps and current scientific and common names.

FishMap has a million and one uses for everyday fish lovers, such as finding out which fishes occur at your local fishing spot, creating a personalised pictorial guide or identifying the fish you spotted during a dive. Researchers can examine the range of a threatened species, or figure out what occurs in a marine reserve. Commercial fishers can find out what fishes occur at different depths in the areas they fish, or even determine the possible species composition for catches of any fishery in the waters of Australia’s continental shelf and slope.

Australia’s marine biodiversity is among the richest in world, but before FishMap there was no easy way to generate illustrated species lists for any location you choose within Australia’s marine waters. It’s the only resource of its kind in the world that covers virtually all species of fish found in the marine waters of an entire continent.

The tool provides the scientifically known geographical and depth ranges of over 4500 Australian marine fishes – including our 320 sharks and rays. Searches reveal illustrated lists of fishes by area, depth, family or ecosystem. These lists can be printed to create simple guides or, if you really want to get serious about it, data can be downloaded into a spreadsheet for research.  

FishMap on the Atlas of Living Australia provides the geographical and depth ranges of some 4500 Australian marine fishes, including the Clown Triggerfish (Balistoides conspicillum).

FishMap is built on the Atlas of Living Australia’s open infrastructure, which is bringing Australia’s plants, animals and fungi from Australia’s biological collections to everyone.

FishMap was developed by CSIRO’s Wealth from Oceans Flagship and the Atlas of Living Australia. Try it for yourself at: http://fish.ala.org.au

The Atlas of Living Australia is an initiative of Australia’s museums, herbaria and other biological collections and is supported by the Australian Government through the National Collaborative Research Infrastructure Strategy, the Super Science Initiative and the Collaborative Research Infrastructure Scheme.

Advisor to the Atlas of Living Australia

By Lee Belbin

I like good wine. Fortunately these days, Australia has a huge number of excellent value wines. After many years enjoying Australia’s wonderful Shiraz, I’ve transitioned through Cabernets to Pinot Noir. However, finding good Pinot Noir is a lot harder than finding good Shiraz.

So that brings me to the point of this article. Maybe you want to discover wineries that are likely to produce a good wine? Maybe you want to grow your own? If the latter, note what a wine grower friend of mine once said: Wine is 33% grapes, 33% winemaking and 33% marketing. The remaining 1% is probably luck.

Can the Atlas of Living Australia be used to find locations of environmental conditions suitable for a specific species? As you have probably guessed, the answer is “Yes!” We can’t help you with winemaking or marketing, but we can (among many other things) help identify areas that could/should produce wine (or anything) that you may like.

The Basics

The Atlas of Living Australia has two basic types of information about Australia’s living things: Species and Environments. As of November 2012, we have over 35 million occurence records about the location of species. People over centuries have recorded what species they observed or collected, and the Atlas has worked hard over the past five years to try and get as much of this data together online in one place. This task continues.

We have a lot of information about species, but one of the most important is “Where do they occur?” The Atlas has also integrated nearly 400 environmental layers. These layers have been collected and integrated into our Spatial Portal because we believe that they are likely to have some relationship with species. We know that the location of species is controlled at least in part by some of the environmental characteristics of these layers.

For example, we know that trees will not grow above the ‘tree line’: the altitude where it gets too cold for them to grow let alone reproduce. We also know that plants and animals require water: not too much and not too little. So each species occurs in an envelope of environmental characteristics.Each environmental layer is a map linking location and environment.

If we know the location, we can identify its environment. The opposite is also possible with the Atlas: If we know the environment, we can find the location/s where this environment occurs.

That’s the key to this exercise: If we know WHERE (good) Pinot Noir (or anything else!) is produced, then we can find out what environment it prefers, and the locations of these environments.

Find the Target Areas

The first step in this study is to locate one or more wineries that you think do it best. In this case, I have selected a few locations in the Yarra Valley because it is the area that produces my favourite style of Pinot Noir.

I’ve also used random coordinates within the area to avoid identifying any particular wineries, but these locations are typical of good Pinot territory. The easiest way to find the location of the wineries is to use either the Spatial Portal or Google Maps.  Use the web to find the address and then find the latitude and longitude (in decimal degrees). Repeat for each winery that produces what you like.The next step is to enter those coordinates into Excel or the equivalent and save the file as a type CSV (comma separated variables).

The first column should contain the name of the first winery. The second column contains the longitude in decimal degrees while the third column is the latitude of that winery in decimal degrees. You can add as many wineries as you like, but remember that they should all have one thing in common – that they grow the best of their type as far as you are concerned.

Below is an example of what the contents of that file may look like.

ID

Longitude

Latitude

Winery 1

145.64

-37.80

Winery 2

145.56

-37.79

Winery 3

145.59

-37.77

Import the Target Locations and Export the Environmental Data
(in one step)

The next step is to import the CSV file into the Spatial Portal of the Atlas of Living Australia and find out what the environment is at these locations. Select Export | Point sample. This will initiate a dialogue to import our points and then append their environments.

The Spatial Portal’s point sampling option

The first question in the process is “What area?” Use “Current extent” which should be Australia by default. The next step is usually to select one or more species and to have the locations of those species used as the sample. For this exercise however, we will use the locations of our wineries as a substitute for species locations. In the Spatial Portal, you can import the location and a bunch of associated features of any type of point observation, species or otherwise. For example, in the Case Study on Wind Farms, we imported the location of the wind farms as if they were species locations (which in a sense they are). Select the option Import points, and then at the next step, enter the name of the points, let’s call it Wineries. The description is optional.

Current extent

Sampling option 1: Use current extents (Australia)

Import points

Sampling option 2: Import our tartget points

Sampling dataset name

Sampling option 3: Name our tartget point dataset

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

We could have used another Spatial Portal Option to separately import the points and plot them (Import | Points), and then export the points with the environmental data attached (Export | Point sample – as we are doing now). We will cut corners by doing the import and export in one go.

Select the Environmental Factors

We next come to the hard part – figuring out which of of the hundreds of environmental layers in the Atlas would be relevant to defining the environment that characterizes the best growing area for Pinot Noir grapes.

One surprising outcome of research examining the hundreds of environmental layers is that a small number of relatively independent layers seem capable of defining Australian environments. One reason for that is that most of the environmental layers are related: One layer can usually substitute for many similar layers. While that is a topic for another Case Study, suffice to say that it appears that five well-chosen environmental layers seem to be able to define the environment of most areas of Australia (see Williams et al. 2012). Note: We know less about the marine environment and consequently have fewer marine than terrestrial layers.

For simplicity, we will use a predefined suite of five relatively independent layers that appear to cover Australian land environments: Use “Best 5 Williams 1960 centered climate layers.” Ideally, the species of interest should be researched to identify the environmental factors that it prefers. As well as temperature and rainfall, we would expect soil conditions, slope and aspect to be significant when it comes to grapes (terroir).

Environmental layers

Selecting our environmental layers: Use "Best 5 Williams 1960..."

When the process is complete, we will have a file called Wineries.csv. When we examine the exported file, we can see that the Spatial Portal has appended values of the five layers to the right-hand side of the table.

ID

Longitude

Latitude

Evaporation – month min

Precipitation – driest month

Precipitation – equinox   seasonality ratio

Precipitation – spring or   autumn season

Water stress index – month   max

Winery 1

145.64

-37.80

32.01

67.00

1.30

0.30

81

Winery 2

145.56

-37.79

31.83

66.00

1.26

0.26

81

Winery 3

145.59

-37.77

31.77

66.40

1.28

0.28

81

There is very little difference in environmental values of the five layers between the three different (fictitious) winery sites. This is not surprising as I selected three random locations in the Yarra Valley of Victoria and therefore one would not expect much environmental difference based on these characteristics.

Generate the Envelope

The next step uses these values in the Spatial Portal to find out where geographically these environmental conditions may also occur in Australia. We will use a feature of the Spatial Portal for defining areas called an Environmental Envelope, as noted above. This envelope defines the environment of our preferred Pinot Noir wine based on my sample points in this case.

We need to define the upper and lower limits of the environmental values. For this study, let’s use the following values

  • Evaporation – month min (31-33)
  • Precipitation – driest month (66-68)
  • Precipitation – equinox seasonality ratio (1.2-1.4)
  • Precipitation – spring or autumn season (for this exercise, let’s skip it)
  • Water stress index – monthly  max (all the same so let’s skip this environmental factor as well)

These values provide a slightly broader envelope to allow for measurement errors and environmental variation. In the Spatial Portal, go to Add to Map | Areas and then select Define environmental envelope. Enter Evaporation – month min in the search box and then enter the lower and upper bound values for this layer (31.5 and 32.5) and then press the button Update species count. The map will be redrawn to display those environments and you will get a species count, in my case of 14,870. What the Spatial Portal is saying is that there are 14,870 species within those environmental ranges in Australia.

Add the remaining two layers, each time entering the ranges and pressing Update species count. When done, we have 994 species. Note this this number will be dynamic, reflecting additions to the Atlas over time. Changing the envelope by even small values will usually result in quite different counts of the number of species.

Envelope parameters

Environmental envelope parameters

When the count has been updated, we have the definition of the environmental envelope. Press Next and the area that encompasses those environmental conditions will be mapped. To see the areas more clearly, increase the opacity of the area layer (top left on the window, slide the slider bar far right) and then select the Map options layer and select Minimal to use the Open Street Maps base map.This base map is simpler and will better display the target areas.

It is not surprising that you can see a number of areas in the Yarra Valley identified. You will however also see a number of areas near Nurran in eastern Victoria that look promising and an even smaller set of areas near Rawson mid-way between the Yarra Velly and Nurran. That’s interesting.

Geographic extression of the environmental envelope

The geographic expression of the environmental envelope

Envelope areas near Nurran, Victoria

The environmental envelope near Nurran Victoria

Summary

If you can identify the locations where your target species like to be, it is then easy to use the Spatial Portal of the Atlas of Living Australia to identify all areas within the Australian region where those environmental conditions occur. You may get some surprises.

Reference

Kristen J. Williams, Lee Belbin, Michael P. Austin, Janet L. Stein & Simon Ferrier (2012): Which environmental variables should I use in my biodiversity model? International Journal of Geographical Information Science, DOI:10.1080/13658816.2012.698015

About the Author

Lee Belbin led the team in the development of the Atlas Spatial Portal, and is now Scientific Advisor to the Atlas of Living Australia. Lee started working life as an exploration geologist in Australia and Canada in 1970. In 1972, he spent 6 years in research and teaching analytical geology at the Australian National University.  From 1979 to 1995 Lee’s research moved to quantitative ecology at CSIRO, with the last three years focused on project management.  From 1995 to 2005, he established and managed one of the world’s first multidisciplinary science data centres at the Australian Antarctic Division. During this time he developed national and international policies and methods for information management and state of the environment reporting. For the past 6 years, his company (Blatant Fabrications Pty Ltd) has focused on managing national and internal projects related to sharing scientific information. Lee has published more than 100 papers on geology, ecology, information management and policy.

PhyloJive (Phylogeny Javascript Information Visualiser and Explorer) is a web based application that places biodiversity information aggregated from many sources onto compact phylogenetic trees. PhyloJive:

  • is entirely client-side
  • renders in the web browser on a HTML5 canvas
  • requires no plugins
  • is open source
  • works in current versions of all major browsers
  • is built on the InfoVis JavaScript library

The project is the brainchild of Garry Jolley-Rogers and Joe Miller and was developed by Temi Varghese and Garry Jolley-Rogers as part of the Taxonomy Research & Information Network (TRIN) – see the original project page, original code repository and ALA code repository. The ALA has contributed to the PhyloJive codebase to integrate a number of web services: occurrence data, maps and character data from Identify Life. This work has been undertaken with help and advice from Joe Miller.

The following screen shot shows a phylogenetic tree for the Acacia genus.

The coloured 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 coloured 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.

 

Importing characters from Identify Life

The ability to import characters from Identify Life is illustrated below. In the “options” tab, click the button labelled “Load” (currently only available for a small number of taxa groups). Once completed, the new characters can seen in the “Character” tab via the drop-down menu.

Mapping

Another new feature is the ability to view a map of occurrence records for a given taxon or ancestral node (map will display all the “leaf” taxa for that node).

Furthermore, the colouring of the dots on the map can be changed from the (default) “by species” to any character available on the tree. In this way it is possible to get a geographic representation of the different possible character states (values).

 

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.

Spatial Portal PhyloJive integration

Spatial Portal PhyloJive integration

These are just a few of the features in PhyloJive. A beta version is available at http://phylojive.ala.org.au/.

Its now possible to view and work with a list of species layers for a genus or higher taxon through a OGC compliant desktop tool such as uDIG or ArcGIS.This allows users to render the data for multiple species on a map within a desktop top with some styling options for the layers. Links to WMS server GetCapabilities documents are on species and higher taxon pages. To retrieve a list of species layers, first navigate to a higher taxon e.g. Acacia

Left panel on species page

Left panel on species page

Clicking the “JSON/WMS/RDF” button on the left hand panel will give the following popup which includes a link to a WMS GetCapabilities document.

This document can then be used in uDIG to retrieve a list of layers available for this higher taxon.

Species layer listing in uDIG

Species layer listing in uDIG

These tools will then allow the rendering of multiple layers.

Multiple species layers

Multiple species layers in uDIG

Individual record information can be retrieved through tool.

Record information

Record information

Below is a screenshot from ArcGIS.

For more details on the WMS services, there is some documentation here.