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

World Wildlife Day 2021

Written by: Cole White


World Wildlife Day logo - Stylized globe with silhouettes of plants and animals


This year's UN World Wildlife Day celebrates forest-based livelihoods worldwide with the theme  'Forests and Livelihoods: Sustaining People and Planet'.


I grew up a family who hunted, fished, and worked in the woods. Later, like many young Canadians, I laboured as a piecework tree planter in the Boreal Forest. But even people I know who have lived their lives in Canada's most urban neighbourhoods feel a connection to woodlands—for example, my Torontonian friends who feel a sense of integration when they visit High Park, the ravines of the Don River, or the Rouge Valley.


Forests are a cornerstone of Canadian life.  Everywhere, plants, microbes, birds, fish and a myriad of other creatures—including us—exist as part of a rich biological schema including forests. In Canada, forests sustain our culture, economy, spirituality, and livelihoods in ways that make this land and its people what they are.


Thirty-nine percent of Canada's land is forest, and this represents 9% of the world's total forests. The future is unwritten, but these numbers tell us that state of Canadian forests is a major variable in how climate change will play out worldwide.


Of course, it's a given that the changes we're already seeing—including severe wildfires, loss of ecological diversity, and the proliferation of invasive species that threaten tree populations—are expected to become more extreme in the coming years.


Adding to this, economic changes due to the pandemic, evolving consumer demands (for example, the decline of print newspapers and magazines), and international competition show that the preexisting commercial relationship between Canadian forests and people won't be the way of the future.


World Wildlife Day 2021 poster by Gabe Wong - Illustration of Indigenous people, plants, and animals from different cultures


Increasingly, many Canadians are recognizing what forests give them, and asking what they can do in return. To me, this year's World Wildlife Day theme (and this inspired illustration for the event by Gabe Wong) expresses a hope that our global communities are affirming their relationships with forests and finding constructive ways forward that honour our interdepedence.


What's happening right now in Canada to support this? Our country's issues are diverse and so multifaceted, but these are a few trends I've noticed recently:


Indigenous Forestry

Indigenous forest management systems offer expertise informed by thousands of years' experience working with this land. The most recent Canadian census reported that 70% of Indigenous people in Canada live in or near forests. (I've also seen similar statistics for other parts of the world, and globally.) Increasingly, Indigenous people are reclaiming portions of their original territories and asserting their right to participate in self-governance, including forest management.


Indigenous involvement in sustainable natural resource management is helping to bring socio-economic benefits to communities and maintain cultural, recreational, and spiritual connections to the land. As reported beautifully in the National Observer, residents of B.C.'s Tŝilhqot'in Nation are using clean energy to develop a new land, water, and wildlife management area, supporting self-determination within their communities.


Coastal Guardian Watchmen also provide a model for what responsible land stewardship can look like in Haida Gwaii.


It's exciting to see collaborative efforts undertaken to synergize traditional ecological knowledge (TEK) and settlers' science-based understanding of nature as complementary information systems.


In a recent lecture, Indigenous scholar and assistant professor Myrle Ballard at the University of Manitoba described how Indigenous expertise can inform scientific work.


The viewpoint has also been expressed poetically in the best-selling Braiding Sweetgrass, by botanist Dr. Robin Wall Kimmerer, who espouses radical gratitude to nature by asking that humans consider the question, 'What can I  give in return for the gifts of the earth?'


Designing for Forest Health

Landscape architects and horticulturalists are inventing and adapting design models that enhance vitality for people and forests.


Miyawaki Forests: Image of tree with captions: Stores carbon, Feeds life, Builds soil, Counters climate change, Cools heat island, Improves health, Cleans air, Dampens sound pollution, Intercepts rainfall, Offers habitat


Planting individual trees is great, but what if you could fast-track the growth of a mini forest community in your neighbourhood? Network of Nature is piloting a new project on using the Miyawaki Forest technique to do just that in Canada.


Wise Use of New Technology

Emerging technologies have their place in this work:


Remote sensing and artifical intelligence can give us new eyes in the sky to monitor our expansive Boreal Forest for extreme wildfires.


Geographic Information Systems (GIS) analysis and interpretitive web cartography are being used to understand and educate Canadians about the value of our northern peatlands.


Ex-situ conservation methods carried out in sterile labs are providing hope for at-risk species, with researchers developing tissue culture and seed banking methodologies to preserve genetically unique local flora.



I think that Gen Z will grow up more attuned to ecological issues than any previous generation. One educational resource I noticed recently is this kid-friendly website, which includes a colouring book, advocating for the conservation of Wisqoq (Black Ash) populations in our eastern forests.


Black Ash

(Fraxinus nigra)

Black Ash is native to Eastern Canada and is used in traditional basket weaving. Populations are currently under threat due to the proliferation of Emerald Ash Borer.


View on Network of Nature

Black Ash


This blog post is a snapshot of my personal reflections, and I'm sure I don't have all the pieces of the puzzle. Maybe you have something to add about how Canadians and forests can work together, or where this is all going.  Do you know of something I should have mentioned here? Let us know!


For more information about World Wildlife Day events, which include a film festival, check out the offical website.


Connecting to Nature in a Time of Crisis

Written by: Cole White


The COVID-19 outbreak is an exponential crisis, where each of us can literally save lives in our communities by heeding the precautions recommended by the WHO and Health Canada to reduce its spread.


We hope you're all doing your best to stay safe and healthy. A connection to nature can help reduce stress and enhance mental health, so we've prepared a list of resources and recommendations to help us all get through this time.



Any book you can dream of can be ordered online in hard copy or ebook form. Also, while your local library may be closed, you may still be able to check out ebooks or digital audiobooks on their website. Here are a couple of our reading recommendations:


An Orchard Invisible: A Natural History of Seeds by Johnathan Silvertown
Seeds piqued my interest while I was working as a lab technician to help develop seed bank technology in Nova Scotia. This book about the evolution, genetic beauty, and surprising diversity of seeds will be compelling to home gardeners and scientists alike.



Gardening Your Front Yard: Projects and Ideas for Big and Small Spaces by Tara Nolan

Janel says, 'Mari-Ann is currently using her extra time to read our friend Tara Nolan’s newly released book and is loving it.'


Seed to Seed: The Secret Life of Plants by Nichlas Harberd
The author uses a diary format to follow a single Arabidopsis thaliana (a common weed often used in scientific studies) specimen throughout its entire lifecycle. Sketches and storytelling are used to illuminate plant biology and meditate on the beauty of natural processes.


Bringing Nature Home by D. W. Tallamy

Summer says: 'Once you have read “Bringing Nature Home” and start making changes in your own back-yard, you will soon want to buy a copy for every friend and family member to help your efforts multiply. The review on the front of the book says it all, If you have a backyard, this book is for you.'



Online Resources

While museums and botanical gardens may be closed, you can still delve into natural history for free online:


Emily Dickenson's Herbarium
The renowned poet was also a skilled gardener who independently studied plants at a time when women were excluded from the scientific community. Harvard has made a high-quality digital version of the herbarium she created in her youth here.


Emily Dickenson's Herbarium

The Cotton MS Vitellius C III

Network of Nature cannot help you find which plants grow best in dragon's blood, but this Old English manuscript, made available by the British Library, can do that and then some. An interesting view for those interested in botany and medieval history.


The Cotton MS Vitellius C III


Create a Plant List with Network of Nature
Create a free account on the Network of Nature website, filter and search to find the right plants for where you are, and develop your own custom plant lists. Lists can be saved, downloaded, and printed!



The National Film Board of Canada
The NFB has many high-quality plant films and documentaries going back over five decades! All of these are available to stream for free in your browser.


Kingdom of Plants 3D
This David Attenborough documentary features as much diversity as an episode of Planet Earth, but it's all shot in a single location -- the world-class Kew Gardens in London.



Get Outside

Note: Please check the recommendations of your public health professionals for this one! In some cases, it may be advisable to stay indoors.


Christina says, 'Nature is one of the few things is still open for enjoyment. Go for a solo hike or jog in your favourite natural space. Studies have shown that immersing yourself in nature helps to reduce stress and improve mental health (something we all could use right now!)


Not only that, but maintaining physical activity and getting some good ol’ Vitamin D is important while we are all cooped up inside for the near future. Make it a time to reflect and be calm, or exert pent up energy or anxiety that many of us are feeling these days.


Hiking in Western Canada


AllTrails is a great (and free!) app that shows you trails in your area, and allows you to filter for less popular spots as we all try and maintain social distancing. As a safety precaution, be sure to carry your cell phone and have a friend or family member aware of your whereabouts if you do endeavour out alone.'


Forest (App)

Summer says, 'I personally find it very hard to “unplug” especially at a time like this when you want to constantly check the news for updates, not healthy! I use this app to temporarily lock my phone to stop me looking at it, it grows a virtual tree that will die if you stop before your time is up. Bonus, you get points that can be redeemed to purchase a real tree the company will plant through a tree planting initiative! '


Submit Photos to Network of Nature

Do you have any photos in your collection of plant species you've identified? If you want to help Network of Nature's mission, now would be a great time to see if you can help us fill in the gaps in our database. Use the Submit a Photo form, or Contact Us directly if you have a larger collection you'd like to share.


Join the Conversation

Connect with us on Facebook and Instagram, leave a comment, and let us know how you're connecting with plants and nature during this time.


Take care of yourself and your loved ones. And if you can, let a connection to nature help you be resilient.

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