The case for using geography to understand phenology

 Alexandra Permar and Conor Flynn collaborated on this project.

Calochortus is an astonishingly diverse genus of flowering monocots, with common names that include Mariposa lily, Sego lily, and globe lily, as well as pussy ears, fairy-lantern, star-tulip, and others.  Their center of diversity is in CA, which has 48 out of the 78 total species in the genus.  In Arizona, there are 6 species, ranging in color from white, to pink, to yellow, and sometimes orange, with diagnostic darker markings on the inner base of the petals.  

    

    This genus in Arizona makes an interesting case study of biogeography and phenology because each species occurs in a relatively distinct (but overlapping) elevation and geographic location.  Also, because the flowers are very showy, there are more than 2,400 Research-grade observations documented on iNaturalist.   

    The plant grows quickly from underground tubers in the spring, flowers quickly, and then dies back; the growing stem and then the seed heads are relatively inconspicuous and are rarely photographed.  This means that almost all of the iNaturalist observations are of the flowers, which makes studying the phenology easier because there is less work needed to annotate images as flowering or not flowering.  Nevertheless, we still reviewed observations and annotated and removed any photographs that didn't show flowers from the phenology analysis below.  

Methods 

Research-grade Calochortus observations in AZ were exported from iNaturalist and processed in Excel and graphed in Excel and Tableau.  iNaturalist Research-grade observations are used for research, but observations with inaccurate locations can lead to misleading analyses and must be removed.  

A total of 2350 observations were exported.  Taxa were classified by species (even though subspecies IDs exist for several hundred observations).  Cleaned records with geopositional accuracy > 1000 m (excluding blanks; there are 594 blanks).  Removed 61 records with geoprivacy obscured. (In iNaturalist, obscured geoprivacy impacts the geopositional accuracy of an observation to +/- 500 square kilometers.)  8 observations were noted as not flowering and were removed from analysis.  After cleaning, the database contained 2066 records (observations).  This shows that about 88% had location precision that met our inclusion criteria.

 Calochortus kennedyi had the most observations (782),  C. ambiguus and C. flexuosus tied for 2nd most observations (534), while C. aureus (148) and C. nuttallii (61) had the least number of observations. 

Geocoding Elevation

iNaturalist does not record elevation of observations, so it is necessary to intersect the observation points with a Digital Elevation Model in GIS.  Observations were added to ArcGIS Pro and displayed using their XY coordinates.  Connect to elevation in Esri AGOL Living Atlas : Ground Surface Elevation - 30m (image service / raster DEM).  Use Geoprocessing tool Extract Multi Values to Points ( Need Spatial Analyst license).  Copy resulting data back to excel. 

        Tableau Public was used to graph data.  Calochortus Bio-Geo-Phenology | Tableau Public

Results: Biogeography and Elevation

    Ordered by average elevation, Calochortus kennedyi and C. flexuosus are the lowest elevation species, C. aureus, C. ambiguus, and C. nuttalli occur at middle elevations, and C. gunnisonnii occurs at the highest elevations.  

iNat allows visualization of biogeographic comparisons.  C. kennedy (blue) is clearly visible at lower elevations along the foothills of the AZ mountains, and then extends to the West beyond the distribution of any other species.  C. flexuosus (green) is also visible to the NW of AZ, extending through central AZ in the lower elevation valleys of the Verde, Salt, and Gila rivers.  C. gunnisonnii (purple) is clearly visible in Colorado, barely extending down to the high country in AZ.  C. aureus (pink) stakes out a unique territory on the Navajo nation in NE AZ and SE Utah. C. ambiguus (red) is found throughout the mountains and high country of AZ.  

 Graphing both latitude and elevation help to illustrate this biogeographic comparison.  In the graph below, it can be seen that C. kennedyi is the most southerly of our Calochortus, and occurs at the lowest elevations.  C. flexuosus occurs farther north, but also at low elevations.  C. ambiguus marks out a consistent territory at higher elevations than other species, depending on elevation. Gunnisonii is a clear outlier, occuring only at high elevation in our study area.  There is a fair amount of overlap between C. aureus and C. nuttallii.

        This biogeographic comparison can help differentiate similar-looking species.  There are 4 white Calochortus in AZ.  C. gunnisonni is clearly only a high elevation species, although C. ambiguous can also occur at high elevations.  In the northern part of the state, C. flexulosus occurs at lower elevations, C. nuttallii at middle elevations, and C. ambiguous only occurs at the highest elevations. 

Results: Phenology

Overall, for Calochortus species in AZ, flowering begins at low elevations around week 13 (last week of March) and progresses to higher elevations, generally wrapping up around week 29 (third week of July).  Flowering species composition changes from C. flexuosus and C. kennedyi to C. ambiguus, with C. aureus and C. nuttalli thrown into the mix.  C. gunnisonni (barely visible at the far upper right) is, of course, the last to flower.  This chart also highlights how C. aureus is mainly restricted to 1600-1800 meters ( 5200-5900 feet).  

    Calochortus ambiguus shows the strongest relationship between elevation, latitude, and flowering date.  Based on this scatterplot, we were able to confirm that the location is not accurate for the observation at the far left side of the plot. 

Calochortus kennedyi, C. aureus, and C. flexulosus do not show as strong of a pattern, and C. gunnisonnii did not have enough observations in AZ to analyze.  

Example of C. kennedyi:

Graphing flowering week of C. kennedyi separately for Latitude and for elevation shows that there is some pattern, but it is clearly quite week.  The R squared values for these charts are 0.22 and 0.12.  Interesting, it looks like flowering actually starts at middle elevations (around week 11), then flowers appear at lower and higher elevations (week 16), until finally only the higher elevations are still flowering (week 20).  C. aureus and C. flexulosus show somewhat similar patterns (data not shown).  

Discussion

    There are many possible ecological and data collection reasons for weak r values:

1) Micro-site variation: south-facing aspect may have more impact than elevation.  Whether a site is forested, if there are shadows from cliffs, etc.

2) Genetic variation:  if a single species showed up with 2 distinct populations, that would be evidence for possible speciation or subspecies, but all populations showed continuous variation.  There may still be genetic variation between meta populations, or within single individuals.

3) Flowering period not known: our records only show flowering presence, not the start of flowering or the total period of flowering.  Correlations might be better if we had complete data, but our data is not complete: we only have point observations.  For example, if species A flowers from April 1-30 and Species B flowers from April 28-May 28, a visitor on April 28 would record both species as flowering at the same time, even though they do have distinct flowering periods.