April 30, 2020

Using iNaturalist Phenology Data

I’ve recently started annotating the phenology of iNaturalist observations of Malacothamnus to see how useful this would be for my research. Phenology is most prominent in climate change research at the moment where researchers are trying to document shifts in flowering time due to climate change. It is also useful in assessing possible reproductive barriers between species. For plant groups that can hybridize like Malacothamnus, geographic distance between species is a major reproductive barrier, but for those growing near each other, offset flowering times can reduce gene flow. Using a combination of iNaturalist observations, herbarium specimens, and other data resources, I can get a better idea of when different Malacothamnus are doing what phenologically.

To start, it is worth taking a look at an iNaturalist plant profile where you can see the phenology data displayed. Here is the profile for Malacothamnus fasciculatus var. nuttallii (Nuttall’s bush-mallow) which should look something like this:

If you click on the “Plant Phenology” tab I’ve circled in red above, you can see the phenology data as currently annotated in iNaturalist. If you hover over the phenology chart, you will be shown a legend that tells you what each of the colors mean and will show you the count of each annotation category for the month you hover over. Also note that you can filter by place (top right), so you could compare the phenology of the same species in two or more locations such as San Diego County, CA vs. Orange County, CA.

There are five possible phenology categories. You can include flowering, flower budding, and fruiting all on the same observation. It is common in Malacothamnus to be at all three of these stages at once. “No evidence“ means there is no evidence of reproductive parts. In general, this will mean a vegetative plant, but could also mean the photo is not adequate enough to assess the phenology. “No annotation” is for observations that have not been annotated. If you hit the cog symbol, you will see an option to annotate those observations needing annotation. Pick a favorite plant and give it a try. If you do annotate, make sure you know enough about the plant you are annotating to add all stages that are in the photos and look at all the photos for each observation. If you aren’t sure about one, skip it and annotate a more obvious one.

Let’s look at some examples of what I’ve found so far.



Above is M. fasciculatus var. nuttallii. This is a fairly decent example of when there is a good amount of data. The green area in the spring shows that people have mapped plants when they are vegetative. That is often not the case. You can see both budding and flowering peak in June, but budding drops on and fruit starts to increase in July. There is an interesting gap in September and October. Many Malacothamnus drop their leaves around this time of year to start growing new ones. Is that why there is a gap? Also note that flowering picks up again in November. Some Malacothamnus will keep having sporadic flowers into the fall, though these are usually just a few flowers or inflorescences on plants that are mostly in late fruit.




On the opposite end of the data spectrum is M. helleri which only has a single observation in each phenology category. Slightly helpful, but not much.




The M. fremontii data look great until June, but it appears that starting in July no one wants to record observations of them. Are they so ugly as to be unmappable this time of year or does everyone just go somewhere not as hot?




M. enigmaticus shows some interesting data bias. This species has a peak bloom from June-August, so why does this chart seem to indicate the opposite? Most of this data was collected by Fred Melgert and Carla Hoegen (efmer) who have done a wonderful job documenting M. enigmaticus. However, they focus their hikes on the lower elevation part of the range of the species and live elsewhere during the summer. This is a great example of where lack of data during some months can really misrepresent the pattern of phenology when viewed for the full year.




Above you can see the early flowering M. clementinus (top) compared to the late flowering M. davidsonii (bottom). Note how great it is to have the vegetative data for M. davidsonii, but what happened in May? Why the data gap?


All of the above were all examples of just iNaturalist data. The group I’m most interested in for phenology is the M. jonesii complex which includes M. niveus and M. gracilis. These three species, which are all included in M. jonesii in some treatments, grow adjacent to each other, but appear to have both morphological and flowering time differences that correspond to geography. They also have intermediates. So, if they aren’t good species yet, maybe they are on their way to becoming ones? There wasn’t much iNaturalist data on these, so I combined iNaturalist, Calflora, Calphotos, and herbarium specimen data to produce the following.

There are still some major data gaps, but note that M. jonesii is flowering in March and April while the others aren’t and M. gracilis appears to flower longer than the rest. They do all overlap in May, but my current data shows M. jonesii is known to flower from March 15 until May 15 whereas the earliest bloom day of M. niveus is May 4 and the earliest of M. gracilis is May 5. That allows only 9-10 days of overlap between M. jonesii and the others when M. jonesii may have already been blooming for a month and a half. So, possibly good evidence for at least partial divergence, but note the lack of data in April for M. niveus and M. gracilis. It may be that people didn’t collect then because there weren’t flowers, but there are also many herbarium specimens I haven’t examined yet.


In conclusion, the point of this was to show the very exciting possibilities of iNaturalist phenology data along with some of the possible problems. There are some fairly easy ways to significantly improve this data.

First, adopt a species (or more) that you feel comfortable accurately annotating the phenology on and do so. Are there differences between two related species that grow together or near each other? Are there gaps in phenology that should be filled in? If you do annotate, make sure you annotate all stages found for each observation.

Second, take iNaturalist observations of the same species year around or as long as they can be found. If you regularly visit the same area, you can document the same plant or group of plants once a month (or even more) to see how they change.

Third, if you know of a species near you that has gaps in the phenology data, try to fill them in with your own observations. I’ve provided a few examples of data gaps above, but there are probably gaps for most species.

Posted on April 30, 2020 20:20 by keirmorse keirmorse | 3 comments | Leave a comment

January 11, 2020

Malacothamnus vs. Sphaeralcea

There usually is no issue in telling Malacothamnus and Sphaeralcea apart as Malacothamnus mostly grow outside of the desert and Sphaeralcea grow in the desert. There are however some Malacothamnus that grow in desert transition areas and sometimes grow with Sphaeralcea.

The first thing to look for is flower color, assuming there are flowers. Malacothamnus flowers are never orange. If the flowers are white to pink though, they could be a Sphaeralcea.

If the flowers aren't orange, it's very important to take photos of a side view of the calyx and bracts, stem, leaves, and more. Examples here:
https://www.inaturalist.org/projects/bush-mallows-the-genus-malacothamnus/journal/7179-photographing-bush-mallows-for-identification

To really confirm if you have a Malacothamnus vs. a Sphaeralcea when there is a question, you need to look at the fruit. Below shows the fruit of a Malacothamnus. The whole fruit is called a schizocarp which breaks apart into carpels. In Malacothamnus, the carpels completely separate into two halves.

Below is a comparison of Malacothamnus and Sphaeralcea carpels. The Malacothamnus carpels completely split into to two pieces. The Sphaeralcea carpels only partially open. Also note the net-like pattern on part of the Sphaeralcea carpel. This is sometimes obscure, but Sphaeralcea has this and Malacothamnus does not.

There are currently only four species of Malacothamnus that are known to occur with or near Sphaeralcea. M. densiflorus can be easily distinguished from Sphaeralcea where they grow together based on their longer and sparser hairs. The remainder aren't as obvious and I don't have time to go into detail at the moment, but still usually look different and comparing photos can help. See: M. orbiculatus, M. enigmaticus, and M. fasciculatus. The Sphaeralcea most commonly confused with Malacothamnus is S. ambigua var. rosea.

Posted on January 11, 2020 21:02 by keirmorse keirmorse | 0 comments | Leave a comment

December 17, 2019

Keys to Identify Malacothamnus

I don't have much yet, but there are now links on my website for some keys to Malacothamnus:
http://www.keiriosity.com/malacothamnus.html

Also, Tom Chester and I just put together an illustrated guide to the Malacothamnus of San Diego, Riverside and Orange Counties which you can view here:
http://tchester.org/plants/analysis/malacothamnus/enigmaticus.html

Sample image from the guide.

Posted on December 17, 2019 20:55 by keirmorse keirmorse | 0 comments | Leave a comment

August 04, 2019

Sharing your coordinates with this project

One of the great things about iNaturalist is that your observations can be used in active scientific research. One impediment to this is that iNaturalist automatically obscures the coordinates of observations of taxa listed as rare. There are 16 rare taxa associated with this project, so obscured coordinates really effect how useful those observations are. One of the most important things you can do to help this research is to share your coordinates with this project.

To share your coordinates, go to the main project page here and click on "Join this project" at the top right corner of the project banner. If you are already a member of the project, click "Your Membership".

From here you are given the option to share coordinates with the project. You will be asked "Do you want to make your private/obscured observation coordinates visible to the project curators? " Choose "Yes, no matter who adds the observation to the project." This will make your coordinates of Malacothamnus observations visible to me.

I will use these coordinates to help clarify geographic boundaries of the various taxa as well as to visit some of these populations when I have questions or need more data. Much of what I have done for my research so far couldn't have been done without all the help of the iNaturalist users who have shared their coordinates. So, thanks to all who have shared!

Posted on August 04, 2019 18:35 by keirmorse keirmorse | 9 comments | Leave a comment

July 11, 2018

Animal Associates of Bush Mallows

I just made a companion project to this one focusing on the animals that interact with bush mallows:
https://www.inaturalist.org/projects/animal-associates-of-bush-mallows

Check it out, join, contribute, and enjoy. It should be interesting to see how many and what animals are associated with the genus.

Posted on July 11, 2018 06:05 by keirmorse keirmorse | 0 comments | Leave a comment

June 22, 2018

Bush-mallow Challenge 5 - The Northernmost Bush-mallows

The northernmost bush-mallows are all currently lumped under Fremont's bush-mallow (Malacothamnus fremontii) which includes Malacothamnus helleri and Malacothamnus howellii. Towards the northern end of the range, known locations become sparse. Below is a map which shows historic collections as orange circles and locations I've found as white circles with Xs in them.

It would be very useful to find more locations in these northern regions. Are these really as rare up there as suggested? Are the various forms distinct or do they grade into each other in the intermediate areas? Do they go even farther north? While they go up close to Redding on the west side of the Central Valley, they aren't known north of Amador County on the east side. Is there a reason for this? Can anyone find some northern populations on the east side?

If you are in the area, keep an eye out or specifically go searching for them. Here's a photo of the northernmost form I've found so far.

Relatively recent burn areas are the best place to look. Follow this link for an interactive burn map.

See also my post here on what to focus on if you want to be able to ID a bush-mallow from photos.

Posted on June 22, 2018 01:42 by keirmorse keirmorse | 0 comments | Leave a comment

March 07, 2018

Bush-mallow Challenge 4 - Parish's bush-mallow

Parish's bush-mallow (Malacothamnus parishii) is known only from its type collections from July 20th 1895 in the vicinity of San Bernadino, CA at an altitude of 1000-1500ft. It is presumed extinct as it hasn't been recorded since then and as the majority of the San Bernadino area is now developed.

This may be a distinct taxon or it may just be a form of the common Malacothamnus fasciculatus. The main distinguishing characteristic from Malacothamnus fasciculatus is the leaf shape being not very lobed and having parallel sides. The red lines denote this in the following image of a type specimen. (Update: I think the leaf bases being cuneate and not cordate may be a major thing to look for too.)

Below are scans of two type specimens:

Larger version here).


Larger version here).

As with all bush-mallows, relatively recent burn areas are the best place to look. Here is a map of recent burns in the San Bernadino area. Follow this link for an interactive map.

Here is a list of all collections from the same collector and day. All I can deduce from this is that he visited a wet area that day, but the Malacothamnus might not be from the wet area. If the collection numbers are in order, there is a fire follower in-between wetland taxa, so these may all be from near the same area. The Malacothamnus collection is flanked by dry-land taxa.

See also my post here on what to focus on if you want to be able to ID a bush-mallow from photos.

Posted on March 07, 2018 17:18 by keirmorse keirmorse | 3 comments | Leave a comment

August 13, 2017

Bush-mallow Challenge 3 - Arizona bush-mallows

If you are in Arizona or just south of the Arizona border, there are two possible bush-mallows to look for out there, maybe more. One of these is only known from collections taken in 1852 and the other is a more recent discovery with few known locations. As with all bush-mallows, relatively recent burn areas are the best place to look. Follow this link for an interactive fire map. See also my post here on what to focus on if you want to be able to ID a bush-mallow from photos.

The type specimens of Malvastrum thurberi which is currently a synonym of Malacothamnus fasciculatus are labelled as coming from Santa Cruz Valley, Sonora, Mexico and were collected in July 1852. Based on what I can find so far, this may mean the location was anywhere between Tuscon, Arizona and Santa Cruz, Mexico. All of the Arizona portion of this area was part of Mexico until the year following the collection.

Below is a scan of a type specimen (larger version here).


The second bush-mallow was collected at Spur Cross Ranch Conservation Area in Maricopa County in 2010 and called Malacothamnus fasciculatus. Based on the photos I've seen, these plants look most like southern populations of what is called Malacothamnus orbiculatus from Los Angeles and San Bernadino Counties in California. Gene Sturla has found additional plants in Tonto National Forest near Sycamore Creek which is also in Maricopa County. These were flowering in September. Below are photos of these plants taken by Gene.

(Update 4/1/19) I found one population. These are growing in a burned juniper woodland. This area burned 7 years ago and ~75% of the population is dead, so new populations are probably unlikely to be found in burn areas much over 10 years old. I would expect them potentially in any burned shrubland or woodland, but they do seem to be pretty rare in AZ. Lower elevation plants have been found flowering in late March and early April. These will likely flower in May. Go find more!
Observation here

Posted on August 13, 2017 17:38 by keirmorse keirmorse | 5 comments | Leave a comment

May 25, 2017

Bush-mallow Challenge 2 - horehound bush-mallow

The second challenge is to find some living plants near the type locality of horehound bush-mallow (Malacothamnus marrubioides). If you live in the Friant area or want to go on an adventure, here is some information to help you possibly find this species. Any observations of any bush-mallows from this area would be very useful information as the nearest other bush-mallow observations are over 30 miles away. All other specimens that are currently called horehound bush-mallow are over 100 miles away. Being that disjunct makes me wonder if they actually are the same taxon.

The type locality of horehound bush-mallow is supposedly from Fort Miller which is now under Lake Millerton. It appears that a single specimen was collected and a few other specimens have been made of fragments of this specimen. The expedition this was collected on stopped at Fort Miller for a week at the end of July in 1853. I could find little detail about that week, but I suspect the specimen may just be from the general area of the fort and that they likely went exploring. The elevation of the fort is a bit low for at least one of the species that was attributed to there. Here is the exploration record if interested. It’s pretty cool.

Below is a map (larger version here) which shows the presumed locality as a star. The red areas are recent burns and the best likely locations to search for the plants. Follow this link for an interactive fire map.

Below is a scan of the type specimen (larger version here).

This illustration is from the published account of the expedition. Larger version here.

Here are some photos of what are considered horehound bush-mallow north of the Los Angeles area.

See also my post here on what to focus on if you want to be able to ID a bush-mallow from photos.

Posted on May 25, 2017 04:12 by keirmorse keirmorse | 0 comments | Leave a comment

May 23, 2017

Bush-mallow Challenge 1 - Mendocino bush-mallow

This is the first of several bush-mallow challenges I’ll be posting for this project. If you live in the Ukiah area or want to go on an adventure, here is some information to help you possibly find this species. Any observations of any bush-mallows from this area would be very useful information.

According to the California Native Plant Society, Mendocino bush-mallow (Malacothamnus mendocinensis) is confirmed from only two historic collections near Ukiah, CA, the last in 1939. It is currently presumed extinct, but bush-mallows are mostly fire-followers and there have been no fires near the type locality for a long time. There are some recent burns relatively nearby which may be worth searching though. The best time to find it in flower would likely be May through July based on the few existing specimens.

Below is a map (larger version here) which shows the presumed localities as a star and an asterisk. The red areas are recent burns and the best likely locations to search for the plants. Follow this link for an interactive fire map.

Below is a scan of one of the type specimens (larger version here).

This crop shows the “conspicuously angulate and striate stem” which is one of the key distinguishing features of this species.

See also my post here on what to focus on if you want to be able to ID a bush-mallow from photos.

Posted on May 23, 2017 19:36 by keirmorse keirmorse | 7 comments | Leave a comment