Creating Phylogenetic Trees with Network of Nature

Written by: Cole White


There are many ways of understanding plants. Scientific study, home gardening, ecological restoration work, and traditional knowledge modalities all offer people significant ways to meaningfully connect with plants and gain an appreciation for the services and beauty they offer.


My interest started with growing up in a rural area and being intrigued by the wild edible plants, such as Lamb's Quarters and Mint, that could be found in my backyard. Later I worked at a botanical garden, which got me interested in more big-picture topics like forest succession and pollination. Now, as a GIS technician at Dougan and Associates and part of the Network of Nature team, I often engage with plant knowledge using data, and databases.


A green icon representing a database, surrrounded by illustrated branches and leaves


The species pages you can explore on the Network of Nature website are powered by an underlying database– that is, an organized collection stored and accessed on a computer. This database contains names, photographs, and various traits (such as native and introduced geographic ranges, bloom colour, and compaction tolerance) for about 5,000 plant species that occur in Canada, all stored in a way that is structured and easily retrieved, modified, or analyzed.


While there may be nuances of biology a typical database system cannot capture, and complex questions these technologies cannot answer in full, the beauty of storing information this way is that it allows us to analyze the collected data in ways that can give us useful (or at least interesting) insights, or raise new questions to inspire further investigation.


One question we recently considered is what a phylogenetic tree created from the Network of Nature database would look like and what further research and exploration this could inspire.


A phylogenetic tree (or 'tree of life') is a branching diagram, visually tracing the evolutionary lineage of a set of organisms back to a common ancestor. All of life on Earth could be traced back to a single ancestor this way. Phylogenetic trees created from more specific datasets are increasingly being used in ecological and biogeographic studies that allow us to learn more about biology and evolution.


An early hand-drawn tree of life by Ernst Haeckel

A 19th-century phylogenetic tree.


Phylogenetic trees used to be hand-drafted by scientists, but can now be created quickly and easily using open source tools developed by unselfish computer programmers. I used the R programming language and an R package called V.Phylomaker to generate a phylogeny based on the Network of Nature database, and a Neo4j graph to store and visualize the results.


A modern tree of life based on genome sequencing

A modern tree of life based on genome sequencing.


R is a programming language widely used by statisticians and data analysts. It incorporates machine learning, linear regression, statistical inference, and other techniques to perform data science work that has applications in many different fields.


The R Logo


The things R can do are extended by add-ons called packages. One of these packages is V.Phylomaker, which uses a 'mega-tree' containing data related to all extant flowering plant families to build phylogenetic trees from a simple spreadsheet of plant species information.


A list of species exported from Network of Nature

A list of species exported from Network of Nature.


Neo4j is a type of database that focuses on relationships between entities, rather than just storing rows of data. We thought this would work as an interesting tool to model the relationships between plant species.


To try this out with Network of Nature, I installed the package and used an export of the Network of Nature database as an input for a small R script using V.Phylomaker. The output of this was a phylogenetic tree in Newick format, a mathematical way of representing this kind of data.


Working with Plant Data in RStudio.

Working with plant data in RStudio.


Next, I used a Python script and the Biopython package to read this Newick data and use it to populate a Neo4j graph.


The result was a dataset of interconnected plant species that could easily be visualized, queried, and explored.


A Network of Nature phylogenetic tree visualized using a graph.

A Network of Nature phylogenetic tree visualized using a graph.


We’re excited to continue exploring the benefits of incorporating a phylogenetic approach into the Network of Nature database. We anticipate that capturing evolutionary relationships among plants will help to deepen our collective understanding of the diversity of plant species found across Canada, and advance the tools and approaches that are used in conservation planning, ecological restoration, gardening, and a wide range of other biodiversity initiatives.


Feel free to reach out to our team if you’re interested to learn more about what we’re doing at Network of Nature.


Further Reading

Climate Change Part 1: What Is It?

Written by: Summer Graham 


Climate change – it’s a big subject, one that is regularly discussed, debated, and often feared. In the next two posts we will try to break down the topic, covering some key terms, the impacts of climate change, and what can still be done about it.


Climate vs. Weather

“It’s cold and snowing here – climate change/global warming can’t be real!”


This is a typical argument used during discussions on climate change, and it often stems from a misunderstanding between two key terms – climate and weather.


Weather is the atmospheric conditions that occur over a short period of time (minutes, hours, and days), whereas climate is the long-term regional and global average of these weather events. Climate considers the average temperate, humidity, and rainfall over the span of seasons, years, or even decades. While climate change may result in a shift in weather events, such as stronger rains, prolonged periods of drought, or more severe thunderstorms, a single weather event cannot be used to prove or disprove climate change.



Global Warming vs. Climate Change

The terms “global warming” and “climate change” are often used interchangeably, however here we will be distinguishing between the two. Global warming refers to the long-term heating of the global climate that has been observed since the pre-industrial period (1850-1900). This warming is primarily driven by human activities such as the burning of fossil fuels which increase heat-trapping greenhouse gas levels in the atmosphere, and is measured as the average increase in Earth’s global surface temperature.
Global temperatures have increased by an estimated 1 degree Celsius since pre-industrial times, and are continuing to increase by approximately 0.2 degrees per decade. 


Climate change, on the other hand, encompasses the long-term changes observed in average weather patterns on a local, regional, and global scale. Where global warming is primarily caused by human activities, climate change also acknowledges the variation in climate caused by natural processes.


Although global warming and climate change are widely debated topics even today, there is overwhelming evidence that atmospheric carbon dioxide has exceeded historic levels within the past century, causing a variety of impacts on our climate and environment.


Impacts of a Changing Climate

Warming temperatures and extreme changes in the Earth’s climate have wide-ranging negative impacts on the environment, which in turn impact the flora and fauna of our planet. One of the changes expected to occur over time is the shifting of natural ranges of plants and wildlife as they adapt to a new, warmer climate. Additional impacts include warming ocean temperatures which contribute to coral bleaching and species die off, shrinking ice sheets, retreating glaciers, rising sea levels, more frequent and extreme weather events (e.g. flooding in some areas and drought in others), and an increase in the frequency and severity of forest fires.


Impacts due to climate change are not only a concern for the natural world.  Unpredictable climate and severe weather patterns can also have major impacts to communities and economies. For example,  a changing climate can lead to reduced crop yields and food insecurity in certain areas. Urban cores can be impacted by higher temperatures in concrete-dominated landscapes resulting in increased cooling costs and health problems. Flooding in cities that lack proper infrastructure can result in large-scale death and destruction, with high economic costs to recover. Check out this photojournalism peice by the Toronto Star about extreme flooding in the city in  August 2018, and the impacts it had on the people who live there. Vectors for certain illnesses (such as tick-borne Lyme disease) can also shift their range to new areas causing more people to be susceptible to disease.


As humans, we are more reliant on and intertwined with the natural world than many people are aware of. It is imperative that we learn about and realize these connections so we can start healing our Earth. But where do we start? Part 2 of this blog will be posted in a couple weeks, where we will discuss the impacts climate change can have on our mental health, and ways to help combat it.    


To be continued…


Additional Reading:

NOAA - Climate Change Impacts 

Climate Reality Project - How Climate Change is Affecting Canada

Government of Canada - Climate Change Causes and Effects

Humans and Nature - What Happens When We See Ourselved as Separate from Nature



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