Thesis Defense

1. M Denniey Snyder
Ecological and genetic variation among
populations of Boechera
caeruleamontana sp. nov (Brassicaceae)
from Blue Mountain and Dinosaur
National Monument in eastern
Utah and western Colorado

2. Dinosaur National
Monument
• Quick Facts:
• >1000 native species
• > 200,000 acres
• Elevation range 1448 m - 2743 m
• 23 exposed geographic strata

3. • Fun things in Park
• Josie Morris Ranch
• Josie Morris was a known friend of
Butch Cassidy and the Wild Bunch
• World-famous Carnegie Dinosaur
Quarry
• Private and Commercial White
Water Rafting on Green and
Yampa Rivers
• Freemont Indian petroglyphs and
pictographs
• Stargazing and Hiking

4. Boechera
• Genus in family Brassicaceae
• Has 71 known sexual diploids
and several apomictic (asexual
reproducing) hybrids
• Extent: North America,
Greenland, Far Eastern
Russia
• Conservation Status: 18/109
Concerned 16/109 Sensitive

5. Boechera vivariensis from
Dinosaur National Monument
• Park rockcress is a rare perennial member of the
mustard family known only from the immediate
vicinity of Dinosaur National Monument.
• It is a G4, in global rarity ranking.

6. What makes something
Rare?
• Rabinowitz description of Rarity in Plant Ecology

7. Boechera vivariensis

8. Boechera vivariensis
an apomictic diploid hybrid
Sexual Diploid
“vivariensis”
Typical
B. vivariensis
B. thompsonii

9. Boechera
caeruleamontana sp. nov.
• Populations of Boechera vivariensis
represent two taxa.
• Allphin and Windham are
recognizing Bochera vivariensis and
Boechera caeruleamontana as distinct
taxa.
• The extent and distribution of each
of these two taxa in Dinosaur
National Monument and
surrounding areas is unknown.

10. Sites Boechera vivariensis is known to grow in
Dinosaur National Monument and surrounding
Bureau of Land Management lands

11. Objectives
• Determine the extent and distribution of
populations of B. vivariensis and B.
caeruleamonta.
• Determine the extent and distribution of
genetic variation within and among
populations of each taxon.
• Determine morphologic differences between
each of the taxa.
• Can the species be distinguished morphologically
within and among populations?
• Determine the habitat characteristics and/or
requirements for both B. vivariensis and B.
caeruleamontana.

12. Methods
Genetic analyses
• Leaf samples collected for more than 50
individuals at known population sites of
B. vivariensis.
• DNA extracted from these samples using a
modified version of the CTAB protocol.
• DNA samples analyzed using 15 previously
developed microsatellite loci following the PCR
methods of Beck et al. 2011.

13. Microsatellites
• Biparentally inherited and co-dominant
• Rapidly evolving with many alleles (useful in groups
where speciation has occurred very recently)
• Once appropriate primers have been developed, easier
and cheaper to obtain genomic data with larger
number of loci representing a greater proportion of
the genome.

14. Methods
Morphometrics
• Morphological measurements were taken
for these specimens at each population site.
• In addition the holotype and isotype from
BYU Herbarium were measured.
• Items measured were leaf size, caudex
length, plant height, and floral size.
• When possible the number of
inflorescences were measured along with
the height of the inflorescence. Length of
fruit and number per inflorescence were
also recorded.

15. Methods
Site Morphology
• 20 individuals were selected at each site by
stretching a 40 m transect through the
center of the main population at site. This
individuals were tagged for long term
monitoring.
• Every two meters the closest individual to
the two meter point was tagged and
measured for clump (mat) diameter (two
perpendicular measurements were taken),
average leaf length (three leaves), number
of rosettes, number of inflorescences,
number of flowers per inflorescence,
average number of fruits per inflorescence,
and fruit to flower ratio.

16. Methods
Soil Sampling
• A total of five composite soil samples
were taken across each of the study
populations.
• At two locations this growing mulch,
or duff was sampled instead due to
the fact that the plants were not
growing on soil.
• Approximately 800 ml of mulch/soil
was obtained and turned over to the
BYU Environmental Analytical
Laboratory.

17. Methods
Soil Sampling
• Nutrients tested for:
• Calcium, Copper, Iron,
Potassium, Magnesium,
Manganese, Sodium, Zinc
• total Nitrogen and Carbonates
• Additional tests were done for
pH, organic matter, nitrate-
nitrogen, soil texture, and
electrical conductivity (salinity)
of the soil.

18. Methods
Community Data
• At each site, a 40 m transect was
stretched through the population in
a random cardinal direction.
• Every 2 m a 100 cm2 nested
frequency quadrat frame was placed
above the transect line
• From these data, nested frequency
and cover of species in the
associated plant community were
obtained.

19. Results
Genetic analyses
• Allelic variation at these loci were used to
generate genetic diversity statistics for all
sampled populations.
• It is important to note that all samples belonged
to the sexual diploid, B. caeruleamontana. In all
our sampling across all sites, we did not
pick up the hybrid taxon, B. vivariensis.
• Genetic diversity statistics among sampled
populations of B. caeruleamontana in Dinosaur
National Monument and surrounding BLM
lands. Values were determined using Genepop
4.2. Standard errors are shown in parentheses
below each mean value. Means followed by the
same letter are not significantly different at P≤
0.10

20. Results
Genetic analyses
• FIS estimates for each locus and
each population of B.
caeruleamontana generated using
Genepop 4.2.
• Estimates followed by symbols
are significant deviations from
H-W equilibrium based on the
Markov chain method.
• Some of the loci had no
variation at a site and so those
were left blank.

21. Results
Genetic analyses
• Pairwise geographic distance (above the diagonal) in meters and pairwise FST estimates
for all 15 microsatellite loci (below diagonal) following Weir and Cockerham (1984).
• FST estimates were generated using Genepop 4.2.
• Private Gene flow migrant value (Nm) was 2.16547

22. UPGMA for Sites
• How the sites are related to each other just
considering Genetic data

23. Sites for Morphometrics
and Soil

24. Results
Morphometrics
• Mean values of morphological characteristics collected at study sites
for 20 tagged individuals at each site. Standard errors are given below
the means. Means in a column followed by the same letter do not
differ significantly at P < 0.05.

25. Results
Reproductive
• Reproductive characteristics from tagged plants at ecological monitoring sites for B.
caeruleamontana. Standard errors are given below the means. Means in a column followed by
the same letter do not differ significantly at P < 0.05.

26. Results
Soils

27. Results
Soils
• The placement of the
five ecologically
sampled B.
caeruleamonanta sites on
a soil texture pyramid.

28. Results
Soils
• Values in ppm of elemental nutrients at sampled sites. Standard errors are given
below the means. Means in a column followed by the same letter do not differ
significantly at P < 0.05.

29. UPGMA
• Relationship for Morphometrics and Soils

30. Results
Community
• Heterogeneity measures for all sampled sites of B. caeruleamontana (Young, Al. 2016).

31. Results
Summary
• In all our extensive sampling of sites not a single B. vivariensis located. The only
species we found at the sites was B. caeruleamontana. This suggests that B. vivariensis
is either much rarer than was prior known (possibly now extinct from our sites), or
a rare (possibly recurring) spontaneous emergence that happens in the presence of
the B. caeruleamontana populations.
• The site that was most unique from all the others was our Jones Hole population,
which was statistically different genetically, morphologically, soil pH, and
ecologically. Jones was most different for genetic loci and showed higher
heterozygosity and higher allelic diversity than all other sites. This number was
however much lower than expected.
• At our sites we only found two pollinators (Bombus sp. and Andrena sp.). These
pollinators primarily forage within a single large mats, one clonal patch. Due to
this we saw very little interactions between mats and evidence of inbreeding.
• All but one site was beginning to be colonized and Blue Mtn Road is starting to be
dominated by Bromus tectorum.

32. Conclusion
• Need to relocate B. vivariensis and determine its true
extent.
• Both taxa, B. viivariensis and B. caeruleamontana are
rare and in need of conservation.
• If sites of highest priority must be chosen for B.
caeruleamontana, Jones and Type should be focused on.
• At site Type methods be taken to continue to prevent
Bromus tectorum from coming in and if possible
remove from site Jones.
• Protect sites that are farther from roadways and
tourist areas.
• Large clumps are less important than total number
of individuals for maintaining genetic diversity,
• Long term monitoring of both taxa suggested for all
sites, along with further greenhouse studies in hopes
of determining frequency B. vivariensis.

33. Acknowledgements
• My parents for financial assistance and emotional support
• My committee, Dr. Loreen Allphin, Dr. Ryan Stewart and Dr. Richard Terry, for all their work
• BYU Students Billie Jean Silva, Blythe Spendlove and Kayla Jett in particular but all those that helped in the
greenhouse and plant collecting.

34. Sources
for Research
• Akkaya, M.S., A.A. Bhagwat, and P.B. Cregan. 1992. Length polymorphisms of simple sequence repeat DNA in soybean. Genetics 132:1131-1139.
• Patrick J. Alexander, Michael D. Windham, James B. Beck, Ihsan A. Al-Shehbaz, Loreen Allphin and C. Donovan Bailey. 2015. Weaving a Tangled Web: Divergent and Reticulate Speciation in Boechera fendleri Sensu Lato
(Brassicaceae: Boechereae) Systematic Botany 40 (2): 572–596.
• Al-Shebaz, I. and M. Windham. 2010. Boechera. Flora of North America Editorial Committee, eds. Flora of North America North of Mexico. Vol. 7, pages 226-367; New York and Oxford.
• Al-Shehbaz, I.A., 2003. Transfer of most North American species of Arabis to Boechera (Brassicaceae). Novon 13(4): 381-391.
• Beck, J.B., P.J. Alexander, L. Allphin, I.A. Al-Shehbaz, C. Rushworth, C. Donovan Bailey, and M.D. Windham. 2011. Does hybridization drive the transition to asexuality in diploid Boechera? Evolution
• Doyle, J. D., and E. E. Dickson. 1987. Preservation of plant samples for DNA restriction endonuclease analysis. Taxon 36:715–722.
• Elith, J., Steven J. Phillips, Trevor Hastie, Miroslav Dudík, Yung En Chee, and Colin J. Yates. 2011. A statistical explanation of MaxEnt for ecologists. Diversity and Distributions, 17:43-5.
• Digital Geologic Map of Dinosaur National Monument and Vicinity, Colorado and Utah (GRI MapCide DINO) nrdata.nps.gov/geology/gri_data/gis/dino/dino_geology.pdf
• Falk, D. A. and Holsinger, K. E. 1991. Genetics and Conservation of Rare Plants. Oxford University Press, New York.
• Federal Register.1993. Endangered and Threatened Wildlife and Plants; Review of Plant Taxa for Listing as Endangered or Threatened Species. Vol. 58, No. 188.
• Hamrick JL, Godt MJW, Murawski DA and Loveless MD. 1991. Correlations between species traits and allozyme diversity: in implications for conservation biology. In: Genetic and conservation of rare plants (Falk DA and Holsinger
KE, eds.). Oxford University Press, New York, 75-86.
• Hirzel, A. H. 2008. Using relative capacity to measure habitat suitability. Israel Journal of Ecology and Evolution 54: 421-434
• Lewis, P.O. and D. Zaykin.2001. Genetic Data Analysis: Computer Program for the Analysis of Genetic Data. Version 1.0 (d16c). http://lewis.eeb.uconn.edu/lewishome/software.html.
• LOVE J. M., A. KNIGHT, M. A. MCALEER and J. A. TODD, 1990 Towards construction of a high resolution map of the mouse genome using PCR-analysed microsatellite. Nucleic Acid Res. 18 4 123-4 130.
• Phillips, Steven J., Robert P. Anderson, and Robert E. Schapire. 2006. Maximum entropy modeling of species geographic distributions. Ecological Modelling, 190:231-259.
• Queller, D.C., J. E. Strassmann, and C. R. Hughes. 1993. Microsatellites and kinship. Trends in Ecology and Evolution 8:285-288.
• Rabinowitz, D. 1981. Seven forms of rarity. pp. 205-217 in The Biological aspects of rare plant conservation. Ed. by H. Synge. Wiley.
• Raymond M. & Rousset F, 1995. GENEPOP (version 1.2): population genetics software for exact tests and ecumenicism. J. Heredity, 86:248-249
• Rousset, F., 2008. Genepop'007: a complete reimplementation of the Genepop software for Windows and Linux. Mol. Ecol. Resources 8: 103-106.
• Schaal, B. A., Leverich, W. J., and S. H. Rogstad. 1991. A comparison of methods assessing genetic variation in plant conservation biology. In D. E. Falk & D. E. Holsinger, eds., Genetics and Conservation of Rare Plants. Oxford
University Press, New York. pp. 123-134.

35. Sources
for Research
• Schlötterer C, Amos B, and D. Tautz. 1991. Conservation of polymorphic simple sequence loci in cetacean species. Nature 354: 63–65.
• Soil Survey Staff. 2014. Kellogg Soil Survey Laboratory Methods Manual. Soil Survey Investigations Report No. 42, Version 5.0. R. Burt and Soil Survey Staff (ed.). U.S. Department of Agriculture, Natural Resources Conservation
Service.
• SYSTAT (Systat Software, San Jose, CA) version 13.1
• Utah Rare Plant Field Guide. 2003. http://www.utahrareplants.org/
• Welsh, Stanly L. 2008. A Utah Flora, 4th edition. Brigham Young University Press, Provo, UT, USA.
• Young, Al. 2016. Biodiversity calculator for Simpson and Shannon Indexes. https://www.alyoung.com/labs/biodiversity_calculator.html?numberOfSpecies=18
• Additional diagrams and Pictures:
• Big Horn Sheep on Green River photo courtesy National Park Service
• Technical manual for sampling small mammals in the Arctic
• GEOSC: 10 Geology of the National Parks Textbook 11.2 Dinosaur National Monument. https://www.e-education.psu.edu/geosc10/l11_p3.html