Tuesday, November 15, 2022

Introduced versus Native Species

 Like almost all categories in nature, there are exceptions and ambiguities. 

How do we really know a species is non-native?  It might seem like an obvious category, but if you think about it, the "evidence" of absence before a certain date is just absence of evidence!  I know taxonomists who don't agree that certain species, widely regarded as non-native, are actually non-native.  They just think the species was under-collected before a certain date.  This is especially true when there is no strong ecological or geophysical reason for the species not to have spread naturally.  For example, species that are "native" to Eastern North America, but are considered "Introduced" in Western North America (e.g. American Bullfrog).

What about species that have both native and introduced genotypes?  Phragmites australis is a classic example from North America, where you have to ID to subspecies (often very difficult) to distinguish the native from invasive.  In iNat, if you only ID to species, it will say it is native.  Only the observations that have been ID'd to species have the Introduced tag. 

Other categories include:

Archaeophytes: plants which were probably introduced by humans to an area, but the introduction happened a very long time ago, and evidence is usually indirect. Most introductions before AD 1492 would fit in this category.  

Neo-natives: This is a rather new term denoting species that settle without human assistance in a new region (see Essl et al. 2019).  For example, range expansions due to global warming.  

More discussion:  https://forum.inaturalist.org/t/residency-status-for-archaeophyte-and-neo-native-plants/37252

What is Mitigation?

Different people have different definitions of "Mitigation" in the context of natural resource management, endangered species protection, and wetland permitting.

Technical Definitions
Technically, Mitigation (as defined by CEQ and DOI) includes avoidance, minimization, and compensatory mitigation.  

The mitigation hierarchy also adopts an inclusive definition of mitigation that includes a range of mitigation options.  The mitigation hierarchy is a framework that was formalized by IFC in 2012.  While there are many complexities in implementation, at its core the hierarchy offers a conceptually simple range of mitigation strategies, ranging from preventive (avoiding and minimizing) to remediative (restoring and offsetting).  

Mitigation hierarchy framework.(Source:  Exponent)

Popular Usage
However, many professional resources, including the USFWS webpage on Mitigation, simply define Mitigation as "projects or programs that help offset negative impacts to natural resources, such as a stream, wetland, and species-at-risk."  This definition excludes by omission any preventive mitigation.

As usual, EPIC has a great resource summarizing the different types of mitigation, as well as synonyms that are often used.  According to EPIC, avoidance and minimization are called "conservation measures".  Only if a project is likely to cause take are compensatory mitigation measures proposed under 7(a)(2) consultation.  Compensatory mitigation, which is usually simply called "mitigation" in popular usage, is also called offset measures.

Table from EPIC report linked above.

In conclusion, mitigation can be a confusing concept, even for professionals.  Government agencies are trying to specify compensatory mitigation when that is the subset of mitigation they mean, but even in official publications they often use the simple term mitigation.  When someone says Mitigation they are usually talking about compensatory mitigation, or offsets.  However, when talking about the mitigation hierarchy, other preventive conservation measures such as avoidance and minimization could also be included.  

Friday, November 11, 2022

Popular plants for Monarch butterflies in Northern Arizona

**Updated 11/16/2022 

As of November, 2022, there were 260 observations on iNaturalist of monarch butterflies in the northern half of Arizona - basically everything north of Phoenix.  I analyzed these observations to try to identify which plants are most important nectar food sources.

iNat link.

I filled in the Life Stage annotation for all larva and pupa.  There are 62 observations of larva (caterpillars), 1 observation of a pupa, and 197 observations of adult butterflies.

The number of monarchs photographed each year has declined from a high of 75 observations in 2015 to an average of 55 a year in 2021 and 2022.  Since the number of iNat users and observations has increased more than 100x since 2014, it seems that the last 2 years represent more effort with less observations, indicating a possible decline in abundance.

For the adults, I annotated the observations using the Observation Field "Nectar / Pollen delivering plant" when I could ID the flower the monarch was observed on.  In some cases, the adult could be observed drinking nectar; in many other cases I assumed that a monarch adult resting on a flower was obtaining nectar.

In total, 71 adult monarchs appear to be drinking nectar from flowers that are identifiable to species or genus.  I documented 27 different plant species being used as nectar resources by monarchs.  This is a large diversity of plant species, considering that this data set included only 71 total observations of monarchs on flowers.

iNat link.

By far the most common plant species was Asclepias subverticillata, the common weedy milkweed species of northern AZ, and also a great plant for monarch caterpillars.  It is possible that some adults were just resting on the milkweed flowers in the process of depositing eggs on the plants, rather than drinking nectar.  Either way, clearly milkweed are important to monarchs.  This species is also popular with a diverse group of other pollinating insects.

Several aster species were also common nectaring plants, as well as butterfly bush (Buddleja), a planted ornamental that apparently lives up to its name!

Monarch presence in Northern Arizona is strongly seasonal, with most adults observed in late summer (August-September), so it is not surprising that some of the late summer Asteraceae such as Ericameria, Helianthus, Bidens and Heliomeris are popular nectar sources.  Since monarchs are generalist pollinators, this data could be consistent with opportunistic (no preference) nectaring.

However, there are many other common plant species flowering during September (such as Gutierrezia sarothrae, Dieteria canescens, Datura wrightii, Purshia stansburyana, Verbascum thapsus, Geranium caespitosum, Achillea millefolium), and no monarchs in this data set were observed nectaring on them. This suggests that monarchs do prefer certain species over others.

Also, there is the question whether the adults observed on flowers during August--October are migrating adults, mating adults, or newly metamorphosed adults.  Given that we do see caterpillars in September, and it takes about 30 days for a monarch egg to grow into an adult, it is likely that all three types of adults are making use of nectar resources in Northern Arizona.  

Caveats and Conclusions

Any mistakes or omissions are my own. I may have misidentified some flower species, but I don't think that would change the overall conclusions.

The small sample size limits the conclusions that can be drawn; more observations are urgently needed to better establish monarch plant preferences.  

Also, this data is subject to the biases of  the "citizen scientists" who use iNaturalist to document biodiversity.  They may be more likely to photograph monarchs on showy flowers, in areas near their homes (landscaped yards and ruderal/disturbed natural environments), and at convenient times of day.

Therefore, this study might be best used to help guide planting decisions to support monarchs in areas near where people live.


Thanks to iNaturalist user jdmore who created an excellent wiki explaining how to use the iNat search URLs to filter results, which was a crucial step to analyze this data.

Also, thanks to all of the iNaturalist community, including the 107 people who observed monarchs in the study area, and the 123 people who helped identify them.

Thursday, November 10, 2022

Is measuring biodiversity possible for non-experts?

I’m trying to measure pollinator biodiversity using iNaturalist, but I’m having doubts as to whether this is even possible for a non-expert.

Over the last five years I’ve photographed insects on flowers in my area, with the goal of creating a summary of total pollinator species per plant species per month. I'm using an Observation Field to associate the plant species with the insect Observation:  https://www.inaturalist.org/observations?place_id=1823&user_id=conorflynn&verifiable=any&field:Nectar%20%2F%20Pollen%20delivering%20plant=

I knew from the beginning that this would not be a perfect research study because I’m not systematically sampling the flowers with equal effort and equal time, and I knew I wouldn’t be able to ID every insect, due to the quality of my photographs.

But I hadn’t considered that the level of taxonomic ID could bias the total species counts. Even if I could ID every photograph to Genus, some Genera have dozens of species while others only have a few. Even worse, some taxa have more people helping ID and therefore have more detailed IDs, whereas other taxa have less interest and are stuck at Family level IDs.  

I think this makes comparing pollinator diversity difficult or impossible on iNaturalist. At best I could say something about how many different Genera or Families visit a particular species of plant --  but I’m not sure how important genera- of family-level biodiversity is...

iNaturalist is a great platform for documenting species observations, but now I think the utility of the data is taxa-specific.  For example, I recently went to a talk about rare talussnails and springsnails in AZ, and the speaker advocated using iNaturalist to document observations.  But how could he ID the rare species from iNat photos?  He just does it based on geography.  There’s no way to discover new snail species or new locations on iNat; DNA studies are needed for new populations to ID whether they are a new or existing species. 

I’d also hoped that I might be able to document new specialist pollinator-plant interactions, but I learned in The Bees in Your Backyard (the definitive bee ID book for North America) that even pollen specialists can be nectar generalists, so I don’t know how one would discover specialist interactions from photographs?  Do researchers have to analyze pollen grains on collected bee specimens??

Monday, November 07, 2022

Tree Risk - notes

 Notes from Tree Risk Assessment Qualification (TRAQ) class taught by Kevin Eckert for the Arizona Community Tree Council.  October 2022 

About 25 people are killed each year by falling trees in U.S.

Removal should only be an option when mitigations are not sustainable.  We have an ethical obligation to do no harm.  The benefits of trees are important.  

A risk is meaningless without a time frame.

Imminent - if a tear in the tree is weathered, the failure is not Imminent

Probable - failure would likely occur during normal (expected/seasonal) extreme weather.

Possible - failure would likely occur during abnormal (hurricane, tornado, derecho, etc) extreme weather.


Thicker sap trees tend to compartmentalize better

If sap is oozing, touch and smell it:

Sticky = ok, its sap

Sour = bacteria

Slimy or foamy = fungus

Wet = just water


Tree dying from bottom up is over-irrigation

Tree dying from top down is drought (under-irrigation)


Soil failure vs root failure:  roots in air or roots break and stay in ground

Codominant is not a fault.  

Included bark is a fault because weak area doesn't hold stems.  

Aspect ratio near 1:1 for codom stems is a fault because don't have enough wood to wrap around union.  This is common cause of failure in pines, especially CA fire investigations.


Worse on compression side and at the base.  Hollow poles are strong. Most stress in tree is around the shell, so sapwood carries most weight, not heartwood (which is more brittle).

Heartwood - least concern

Sapwood - will start seeing tip dieback. 2nd worst.

Root - will also see tip dieback.  Not too bad if not structural; crown dieback will balance root dieback.

Basal - worst.  

Types of Response growth:

Reaction wood from tension/compression

Flexure wood from movement

Wound wood - e.g. lip around wound. More growth shows more stress

Likelihood of failure increases/decreases based on load (e.g. wind exposure) / response growth


Reproduction is sign of stress in trees (plants):  orchard trees cut to fruit more, but decreases lifespan.

Vigor/health does not always reduce tree failure risk

Adding N can increase leaf area and stem elongation, but that can increase load on stem and if stem doesn't thicken then can increase tree failure risk, even while increasing tree "vigor".  Sometimes reducing growth (ie use growth regulator) can improve mitigations.

Sheer plane: where tension and compression meet

Cracks: transverse (fiber failure) or longitudinal (with the grain)


Old trees: retrenchment = natural process of aging, shortening and widening = more stable

Trees naturally move with wind.  Mass damping shows importance of inner branches and leaves.  Helps tree stems "undulate like snake in the wind".  Sharp bends or lack of inner leaf area can inhibit natural movement.


New concrete can leach lime/calcium oxate which raises soil pH and can harm some plants if too much

Adventitious branches = "water sprouts" (from topping = non ANSI cuts) = epicormic.  Poor attachments can rip out.

Shigo said:  "don't err on the side of safety….just do it right!"  :: Do the best you can based on your education, training, and experience.  

Wednesday, November 02, 2022

Arizona Monarchs Visit California and Mexico

 Five years ago my wife and I joined other local citizen scientists at Willow Lake for an enjoyable afternoon catching and tagging monarch butterflies.  The tags are small stickers with ID numbers.  They  don't impair the butterfly's ability to fly, but they do let us humans track where they fly to!

A monarch in the hand.

 The Southwest Monarch Study group recently updated their map showing the location of recovered tags.  The straight lines indicate starting and ending locations, not necessarily the meandering paths monarchs take to migrate across the landscape. 

Image from Southwest Monarch Study.  

  Over the ensuing years, those tagged butterflies have turned up as far away as the monarch's overwintering grounds in Mexico. Interestingly, they also visit California overwintering sites.  Most monarch populations can be neatly divided into Eastern and Western populations based on where they spend the winter; Eastern go to Mexico and Western go to California.  But it seems AZ monarchs can go to either, which raises the fascinating question: how do they decide where to go?  Is AZ a meeting spot for different populations, and each return to their home wintering sites, or is AZ a melting pot, a single population where individuals decide each year where to overwinter?

Hopefully this citizen science research will help resolve some of the question marks on monarch migration maps.

Monarch migration map from Xerces.

Monarch migration map from Monarch Watch. 

Monday, October 31, 2022

Fire Retardant Visible From Space

The Bush Fire started on the West side of Highway 87 in Arizona on June 13, 2020.  Drive by strong winds from the SW, it soon spread to the highway median and then crossed to the East side of the highway.  From there, it went on to burn 193,000 acres until it was completely contained on July 6, 2020.
Air tanker drops retardant ahead of fire.  Photo by JDH images.  https://wildfiretoday.com/tag/bush-fire-in-arizona/

Air tankers were extensively used in the initial attack on the fire, and Google Earth images of the fire start location show some interesting features.  These images were taken on June 20, 2020, 7 days after the fire had burned this location.

The fire started on the West side of 87.  Fire retardant strips are visible in several locations.

Where the fire was backing against the SW wind, retardant drops were successful in stopping the spread of the fire.  A small bulge near the top of the image shows where fire crossed the line, but was contained.

Retardant drops on the south side of the fire were not successful in stopping the fire, but may have been instrumental in slowing the fire which allowed it to be stopped at the dirt road.

Retardant drops directly in front of the wind-driven fire were not successful in holding against the onrushing flames.  The fire spread over and around the retardant line in this image.

At another location on the same date, the fire can still be seen actively burning.

Thursday, October 27, 2022

Is Forest Thinning Beneficial for Everyone?

 This Undark article says Pinyon jays are proposed for ESA listing because of forest restoration thinning:

“some bird biologists... are sounding the alarm that even today’s thinning methods degrade pinyon jay habitat. These woodlands are already under extreme drought stress, especially in New Mexico, with predictions for widespread loss due to climate change. And some studies suggest thinned piƱon-juniper forests are less resilient to beetle infestation and drought.

 I participated in a 10-year monitoring study of thinned and unthinned Pinyon-Juniper woodlands in the Manzano mountains.  Our findings were different from those discussed in the study; we found increased soil moisture at thinned plots, which led to richer pinyon nut crops and an increase in pinyon jays.  

However, I'm not arguing that the cited studies are wrong; there may be important site-specific differences between different restoration treatments in different areas.    Some restoration can actually help pinyon jays, we just need to figure out which treatments, and how!

Hopefully, we can all agree that if a treatment isn't making things better for native plants and animals we need to rethink it; just because something is called "restoration" doesn't mean its automatically good.  That's why we need science like this.


Wednesday, October 26, 2022

Upcoming Endangered Species Listing Decisions in Arizona 2022-2027

I found a 5-year workplan on the USFWS site and made a list of all of the AZ species that USFWS will make listing determinations for. 

Its pretty interesting to look at what’s coming up.  Lots of talussnails!  But after the Sonoran desert tortoise (which they decided not to list), I think the next big one is the Monarch butterfly.  

Also interesting that there’s no bumble bee species on this list, as I know they’ve been petitioned.  Of course, this could all change as new species are added to the candidate list and priorities change...



Sonoran desert tortoise

-widely distributed in AZ deserts

- listing decision spring 2022: not warranted


Cactus ferrugous pygmy owl 

-by end of calendar year




roundtail chub


gray wolf (western populations)




Joshua tree 


Quitobaquito tryonia




Monarch butterfly

-widely distributed in AZ

A listing proposal is anticipated by November 2023, with a final listing decision by end of Federal FY2024 (September 2024). 


Las Vegas bearpoppy Arctomecon californica


Pinaleno talussnail Sonorella grahamensis

San Xavier talussnail Sonorella eremita




Ferris's copper butterfly Lycaena ferrisi


ASNF southwest of Springerville


Chisos coral-root Hexalectris revoluta

Sky island mountains


Threecorner milkvetch  Astragalus geyeri var. triquetrus


Grand Wash springsnail Pyrgulopsis bacchus

Kingman springsnail Pyrgulopsis conica




Arizona toad Bufo microscaphus microscaphus

- widely distributed in AZ



Navajo bladderpod Lesquerella navajoensis

- habitat on Navajo Nation


Yuman Desert fringe-toed lizard Uma rufopunctata


Mojave poppy bee    Perdita meconis 


Bylas springsnail Pyrgulopsis arizonae

Gila tryonia Tryonia gilae

Huachuca woodlandsnail Ashmunella levettei


Squaw Park talussnail Maricopella allynsmithi

-populations are on city or county parks in the Phoenix metro area https://explorer.natureserve.org/Taxon/ELEMENT_GLOBAL.2.114155/Maricopella_allynsmithi


Verde Rim springsnail Pyrgulopsis glandulosa





Morton's wild buckwheat  Eriogonum mortonianum


Pipe Springs cryptantha    Cryptantha semiglabra


Source: https://www.fws.gov/media/national-listing-workplan-fiscal-years-2022-2027

More USFWS lists:  https://ecos.fws.gov/ecp/species-reports

Friday, October 14, 2022

Biodiversity on Prescott National Forest

 How many plant species are there in a geographic area?  Previously, I used iNaturalist to calculate total biodiversity for selected areas.  But this method is just a snapshot of the species currently recorded in iNaturalist.  In some areas, people may have already observed most of the biodiversity, while in other areas there may still be much more to discover.

One way to estimate the total unobserved biodiversity of a geographic area is to look at the timeline of species observations.  If more new species are being observed each year, there are likely still many more species to discover, whereas if the number of new species each year is declining, we may be able to fit a decay function that would predict the total number of species that will ever be observed.

iNaturalist offers a couple of ways to find lists of new species.  As an example, I will use the Prescott National Forest in AZ.

The first method: the API function recent_taxa.

According to this method, there have been 57* new plant species observed on the Prescott National Forest in iNat so far this year.  This is filtered for only research grade observations (quality_grade=research).  There are a lot of new observations by experts that just haven’t been confirmed by other experts. *For some reason this returns the species, genus, and family so to get 57 I subtracted repeated taxa (29) from total new taxa this year (86).


The URL code is pretty easy to modify for other places (PNF = 130970) and other taxa (plants = 47126).  Here is more background on API query terms: https://api.inaturalist.org/v1/docs/#!/Identifications/get_identifications_recent_taxa

The second method: download data.

 When searching observations for Prescott National Forest and filtering by plants, iNaturalist returns a page with summary statistics.   This can be downloaded and analyzed in Excel.


 After downloading the data:

1. sort the table from oldest to newest by the observation date column

2. select the whole table

3. use “remove duplicates”, and look for duplicates in only the species name column

The resulting list will show you the first observation of each species.  I then summarized the list by year and created this graph showing the year and number of new plant species recorded in iNaturalist for PNF.  

This method also sometimes returns other taxa than species, so the totals don't quite match between the website, the API, and this method.  Also, this graph is not filtered for only Research Grade observations, but it would look basically the same.  The graph appears to increase over time as more people use iNaturalist to record plant species on Prescott National Forest, up to a peak year in 2020.  Since then the number of new species seems to fall off, although it should be noted that 2021 was a drought year and 2022 isn't over yet.