Population Viability Analysis - Annual Transition Matrices

Metadata:


Identification_Information:
Citation:
Citation_Information:
Originator: Kaye, Thjomas N
Publication_Date: 2001
Title: Population Viability Analysis - Annual Transition Matrices
Geospatial_Data_Presentation_Form: transition matrices
Online_Linkage: <http://fresc.fsl.orst.edu/online/online_docs/kaye/appendix.pdf>
Larger_Work_Citation:
Citation_Information:
Originator: Thomas N. Kaye
Publication_Date: 2001
Title:
Population Viability Analysis of Engangered Plant Species:An Evaluation of Stochastic Methods and an Application fo a Rare Prairie Plant
Geospatial_Data_Presentation_Form: PhD dissertation
Publication_Information:
Publication_Place: Corvallis, OR
Publisher: Oregon State University
Online_Linkage: <http://fresc.fsl.orst.edu/online/online_docs/kaye/thesis.html>
Description:
Abstract:
The data represent transition matrix models for 5 species and 27 populations of rare or endangered plants species in Oregon. Each matrix model represents a one-year transition developed from field observations of mapped individuals. Data are contained in the Appendix of the Larger Work Citation
Purpose:
These data were collected as part of long-term monitoring programs for rare plants in Oregon to document their population trends and conduct population viability analyses.
Supplemental_Information:
Annual transition matrices. The transition matrices are in a condensed format. Each column represents a transition matrix for a single year of observation. The entries in a column of the table are the entries in each column of the matrix, stacked one above the other, beginning with seedling transitions at the top. To reconstruct a square matrix, each column must be reshaped so that the first five entries (or four for Haplopappus radiatus and six for Lomatium cookii) form the first (left hand) column of the matrix, the next five (or four or six, as above) the next column, and so on.
Time_Period_of_Content:
Time_Period_Information:
Range_of_Dates/Times:
Beginning_Date: 1991
Beginning_Time: Unknown
Ending_Date: 2000
Ending_Time: Unknown
Currentness_Reference: ground condition
Status:
Progress: Complete
Maintenance_and_Update_Frequency: None planned
Spatial_Domain:
Description_of_Geographic_Extent: Various western Oregon locales
Bounding_Coordinates:
West_Bounding_Coordinate: -124
East_Bounding_Coordinate: -122.5
North_Bounding_Coordinate: 46
South_Bounding_Coordinate: 42
Keywords:
Theme:
Theme_Keyword_Thesaurus: none
Theme_Keyword: endangered species
Theme_Keyword: demography
Theme_Keyword: transition matrix
Theme_Keyword: population viability analysis
Place:
Place_Keyword_Thesaurus: None
Place_Keyword: Oregon
Taxonomy:
Keywords/Taxon:
Taxonomic_Keyword_Thesaurus: none
Taxonomic_Keywords: Astragalus tyghensis
Taxonomic_Keywords: Cimicifuga elata
Taxonomic_Keywords: Lomatium bradshawii
Taxonomic_Keywords: Lomatium cookii
Taxonomic_Keywords: Haplopappus radiatus
Taxonomic_Classification:
Taxon_Rank_Name: Kingdom
Taxon_Rank_Value: Plantae
Taxonomic_Classification:
Taxon_Rank_Name: Division
Taxon_Rank_Value: Magnoliophyta
Taxonomic_Classification:
Taxon_Rank_Name: Class
Taxon_Rank_Value: Magnoliopsida
Taxonomic_Classification:
Taxon_Rank_Name: Sub Class
Taxon_Rank_Value: Rosidae
Taxonomic_Classification:
Taxon_Rank_Name: Order
Taxon_Rank_Value: Fabales
Taxonomic_Classification:
Taxon_Rank_Name: Family
Taxon_Rank_Value: Fabaceae
Taxonomic_Classification:
Taxon_Rank_Name: Genus
Taxon_Rank_Value: Astragalus
Taxonomic_Classification:
Taxon_Rank_Name: Species
Taxon_Rank_Value: Astragalus tyghensis
Applicable_Common_Name: Tygh Valley milkvetch
Taxonomic_Classification:
Taxon_Rank_Name: Order
Taxon_Rank_Value: Apiales
Taxonomic_Classification:
Taxon_Rank_Name: Family
Taxon_Rank_Value: Apiaceae
Taxonomic_Classification:
Taxon_Rank_Name: Genus
Taxon_Rank_Value: Lomatium
Taxonomic_Classification:
Taxon_Rank_Name: Species
Taxon_Rank_Value: Lomatium bradshawii
Applicable_Common_Name: Bradshaw's desert-parsley
Taxonomic_Classification:
Taxon_Rank_Name: Species
Taxon_Rank_Value: Lomatium cookii
Applicable_Common_Name: agate desertparsley
Taxonomic_Classification:
Taxon_Rank_Name: Sub Class
Taxon_Rank_Value: Magnoliidae
Taxonomic_Classification:
Taxon_Rank_Name: Order
Taxon_Rank_Value: Ranunculales
Taxonomic_Classification:
Taxon_Rank_Name: Family
Taxon_Rank_Value: Ranunculaceae
Taxonomic_Classification:
Taxon_Rank_Name: Genus
Taxon_Rank_Value: Cimicifuga
Taxonomic_Classification:
Taxon_Rank_Name: Species
Taxon_Rank_Value: Cimicifuga elata
Applicable_Common_Name: tall bugbane
Taxonomic_Classification:
Taxon_Rank_Name: Sub Class
Taxon_Rank_Value: Asteridae
Taxonomic_Classification:
Taxon_Rank_Name: Order
Taxon_Rank_Value: Asterales
Taxonomic_Classification:
Taxon_Rank_Name: Family
Taxon_Rank_Value: Asteraceae
Taxonomic_Classification:
Taxon_Rank_Name: Genus
Taxon_Rank_Value: Haplopappus
Taxonomic_Classification:
Taxon_Rank_Name: Species
Taxon_Rank_Value: Haplopappus radiata
Applicable_Common_Name: ray goldenweed
Access_Constraints: None
Use_Constraints: None
Point_of_Contact:
Contact_Information:
Contact_Person_Primary:
Contact_Person: Kaye, Thomas N.
Contact_Organization: Dept. Of Botany and Plant Pathology
Contact_Address:
Address_Type: mailing and physical address
Address:
Dept. of Botany and Plant Pathology Oregon State University
City: Corvallis
State_or_Province: OR
Postal_Code: 97331
Contact_Voice_Telephone: (541) 753-3099
Contact_Facsimile_Telephone: (541) 753-3098
Contact_Electronic_Mail_Address: kayet@bcc.orst.edu
Data_Set_Credit:
This research was supported by US Geological Survey Forest and Rangeland Ecosystem Science Center.

Data_Quality_Information:
Attribute_Accuracy:
Attribute_Accuracy_Report:
During analysis data were repeatedly checked against field data sheets.
Logical_Consistency_Report: No specific tests for logical consistency were conducted.
Completeness_Report: Refer to Methodology
Lineage:
Methodology:
Methodology_Type: Field
Methodology_Description:
ASTRAGALUS TYGHENSIS A total of 15 permanent monitoring plots at five sites were sampled to obtain demographic data from five populations of Astragalus tyghensis. Monitored populations were at sites 4, 10, 13, 25, and 41 (Kaye and Brady 1991). Plot locations were selected by visually partitioning each population into homogeneous areas, then randomly placing plot locations. All permanent plots were 5 x 5 m square, marked in each corner with a 1 m piece of iron rebar protruding at least 30 cm from the soil. The upper left corner-rebar of each plot (facing up-slope) was labeled with an aluminum tag noting plot number. To sample, each side of the plot was marked temporarily at 1 m intervals with nails, and string was tossed back and forth over the plot (looped each time around a nail) to create a grid of 1 x 1 m subplots within the 5 x 5 m macroplot. The location of each Astragalus tyghensis individual in every subplot was mapped and numbered on map sheets. A dot and a corresponding plant number were placed on the map sheets to mark the position of each plant. In some cases, it was difficult to determine whether tufts of plants were clusters of individuals or merely a single plant that had branched below the soil surface, or a combination of these. In these cases, the loose soil was gently excavated and probed with fingers to check for root connections. On a separate data sheet, we noted diameter (cm), length of longest stem (cm), number of inflorescences, and evidence of grazing (yes or no) of each mapped and numbered plant.

To assess seed production, we sampled between 25 and 80 plants at each monitoring site. Plants were sampled at random for number of inflorescences and fruits adjacent to and outside of the permanent macroplots. In addition, whole infructescences were collected at random and inspected for seed set per fruit and insect seed predation. At sites 4 and 41, the number of fruits per plant was measured for all plants in the plots, instead of subsampling outside the plots, because of the relatively low number of flowering plants at those sites. The samples were collected each season when fruits were mature. For each site, we performed linear regressions to determine the number of fruits expected from a plant given the number of inflorescences (for these tests, P < 0.05) (except at sites 4 and 41 in 1992-98, and 4, 10, 25, and 41 in 1999 where fruit production was measured directly). These data were multiplied by the average number of seeds per fruit at each site to give an estimate of the number of seeds produced by each monitored plant. The following formulae were used to calculate the number of seeds produced per plant given the number of inflorescences or fruits [(#inflorescences×regression coefficient for fruits/inflorescences)×average number of seeds per fruit].

For the purposes of the model, the individuals in a population were assigned to categories (stages) based on age (for seedlings only) and size. The number of seedlings produced per plant in each category was determined, and the probability of individual stasis in the same stage or transition to another was be calculated. The transition probabilities were the proportion of individuals in each stage that made the transition to another stage (e.g., become smaller or larger) from one year to the next. We recognized five stages for this species based primarily on stem length: seedling, longest stem <10 cm, 10-20 cm, 20-30 cm, and >30 cm. These stages were defined subjectively after displaying the size data graphically in several different ways. In a few cases, data for a particular stage were lacking for a given year due to absence of that category from the population samples. When this occurred, the column for that stage was replaced by the mean transition elements from all other years.

CIMICIFUGA ELATA We used data from three C. elata populations to derive transition matrices: EUGRASS, EUNORR and WIL032 (Kaye and Kirkland 1994). At each population, we measured all the following characteristics of each plant: number of leaves, number of reproductive stems, and number of racemes. In addition, we mapped and tagged individuals within 40-m on either side of a reference transect. Plants were mapped according to a coordinate system in which the first (x) coordinate is the distance along the reference transect to a plant, and the second (y) is the lateral (perpendicular) distance from the transect to the plant. Because plants usually were found on both sides of the transect center-line, plants to the right of the transect (facing in the direction of the transect) were given positive y-axis ordinates, and those to the left were assigned negative y-axis ordinates. Distances were measured to the nearest decimeter to the base of the plant where it rooted into the soil. Plants were permanently tagged by inserting a stiff wire (12 gauge) into the soil 15-cm away from the plant perpendicular to the transect center-line. The wire was looped at the top and a machine-numbered aluminum tag was fixed in the loop. In this way, each individual was tagged with a permanent and unique number and set of coordinates. Data from tagged plants were used to classify each individual into five stages, including seedling, vegetative with 1 or 2 leaves, vegetative with 3 or more leaves, reproductive (having at least one flower stalk), or dormant (for plants that skipped one or more years then reappeared). As in matrices for A. tyghensis, when too little data were available to calculate transitions for a particular stage, the matrix column for that stage was replaced by the mean. This occurred for the EUGRASS population in which the large vegetative stage was replaced by means in year 2, for EUNORR where seedlings, recuitment, and dormany were replaced by means only in year 4, and WIL032 where seedling and large vegetative transitions were replaced by means in year 1.

HAPLOPAPPUS RADIATUS Ten plots were established at five sites within the Oregon portion of the range of Haplopappus radiatus (Kaye and Meinke 1992). Plots were assigned to a fenced or unfenced treatment by a toss of a coin. All plots, whether inside or outside of an exclosure, were 10 x 10 m square and followed the same basic form. It was necessary to incorporate walk-ways into the plot set-up in order to reach the individual subplots for close inspection. Therefore, each plot was composed of five 1-m wide belt transects alternating with 1-m wide walk-ways. The belt transects were marked permanently with rebar posts anchored at each end. Each transect was broken into 10 contiguous 1 x 1 m subplots in which plants were mapped and measured. Thus, there were five transects of ten subplots each, for a total of fifty subplots per plot (plot 1-out was an exception, with only 25 subplots). To locate the plots for sampling, a meter tape was run from the left post to the right post (left and right as if facing up-hill), and each 1-m segment of meter tape formed the lower edge of each subplot. A 1 x 1 m frame was then placed on the ground (with one edge along the meter tape) to delineate the subplot.

In 1991 the plots were sampled twice, on April 15-18 and July 19-23; 1992 sampling occurred on May 7-10 and July 20-24; 1993 sampling occurred on May 11-12 and July 13-14; 1994 sampling occurred on May 17-19 and August 2-4; 1995 sampling was conducted on May 22-26 and August 7-11; 1996 sampling occurred August 12-16; 1997 sampling was on May 28-29 and August 5-7; 1998 sampling was done on May 19-20 and July 28-30, and sampling in 1999 was conducted on May 18-19 and July 26-29. The early spring samples were conducted primarily to maintain the plots and locate seedlings. All plants were measured and remapped during the summer sample. In every subplot, all Haplopappus radiatus individuals were mapped onto special map forms and numbered consecutively on the map. Data on plant height (cm), length of longest leaf (cm), number of leaves, number of healthy and aborted flower heads (capitula), number of grazed stems, and percentage herbivory by grasshoppers, were recorded onto a second data sheet. In 1991, the density of Haplopappus radiatus was so high at the Lime sites (1 & 2) that we reduced the area of the subplots where non-reproductive plants are mapped and measured to the lower left-hand quarter of the subplots. All reproductive individuals in the entire subplot were mapped and measured in the Lime plots (1 & 2). In addition, only even numbered subplots were sampled at Upper Lime plot 1-out. All portions of all subplots were sampled at the Lookout Mountain Road sites (plots 3, 4 & 5). In 1996, protocol was changed at the Lime sites so that mapping and measuring included all plants in all plots. Each individual was assinged to ne of four stages based primarily on number of leaves and reproductive status: seedling, juvenile(#four leaves), vegetative (>4 leaves and non-reproductive), and reproductive (producing at least one flowering capitulum). These stages were defined subjectively after displaying the size data graphically. Occasionally, no seedlings survived at all in a given population and year, and in others, all seedlings survived. Also, in some plots, no reproductive plants were observed in some years, so no data were available to estimate transition probabilities of this stage class. As above, where data were lacking, we used the average of transition probabilities from the years when these data were available.

LOMATIUM BRADSHAWII We used information from three populations that were part of a prairie burning experiment (Kaye et al. 2001) to collect demographic data on Lomatium bradshawii. All three, Fisher Butte, Rose Prairie, and Long Tom, were within the southwest part of the species' range, in an area west and north of Eugene, Oregon. Three burning treatments were conducted at two of the locations, making a total of seven independent demographic data sets for this species. Permanent monitoring plots were sampled annually. To establish these plots, mature Lomatium bradshawii plants (reproductive or large vegetative) were randomly chosen from throughout the population areas and tagged in 1988. These individuals were numbered, and a subset, ten at Fisher Butte, six at Rose Prairie, and ten at Long Tom, were randomly selected from each treatment area to serve as center points for permanent circular plots (2-m radius). All L. bradshawii individuals were mapped in each circular plot in May or June of each year (prior to burning) from 1988 through 1993. Leaf number, seed production, and umbel number were recorded annually for all tagged plants, including those at the center of each circular plot and outside the plots, and seed production per reproductive plant category was used to estimate per capita seedling recruitment for each reproductive stage. We used a biological classification that combined plant size and reproductive state to classify each Lomatium bradshawii individual into one of five stages: seedling, vegetative plant with one or two leaves, vegetative plant with three or more leaves, and reproductive plant with one, or two or more umbels. Reproductive plants were segregated by umbel number because one-umbel plants rarely produce seed, while two-umbel plants produce seeds on the second umbel, and plants with three or more umbels may produce many seeds (T.N. Kaye, unpublished data). We combined vegetative plants with one or two leaves into a single stage because field observations indicated that plants with one leaf often produced a second leaf later in the year, and therefore leaf number of small plants may be a function of sampling date and/or variation in seasonal phenology, not plant vigor. Seedlings were defined as first year plants, often with cotyledons. All vegetative plants with one leaf were considered seedlings in 1988.

LOMATIUM COOKII Long-term monitoring plots were established at two populations in near Cave Junction, Oregon (Kaye 2000). At each population (Middle and South), 20 plots were randomly placed. These plots were 0.5 x 0.5-m, and all individual Lomatium cookii plants were mapped to their approximate location, given unique numbers, and assigned to the categories defined below. To sample, a 0.5 x 0.5-m frame was placed over the plot and all plant positions were mapped to scale on a map form. Plant categories were seedling, vegetative with 1 or 2 leaves, vegetative with 3 or more leaves, reproductive with 1 umbel, reproductive with 2 umbels, and reproductive with 3 or more umbels. As above, where data were lacking, we used the average of transition probabilities from the years when these data were available .

Methodology_Citation:
Citation_Information:
Originator: Kaye, T.N. and S. Brady
Publication_Date: 1991
Title:
Astragalus tyghensis monitoring, pollination, and germination. First year project status report
Geospatial_Data_Presentation_Form: Report
Publication_Information:
Publication_Place: Salem, Oregon
Publisher: Oregon Department of Agriculture, Salem
Methodology_Citation:
Citation_Information:
Originator: Kaye, T.N
Publication_Date: 2000
Title:
Lomatium cookii population monitoring in the Illinois Valley, Josephine County, Oregon
Geospatial_Data_Presentation_Form: Journal article
Publication_Information:
Publication_Place: Corvallis, Oregon
Publisher: Institute for Applied Ecology
Methodology_Citation:
Citation_Information:
Originator: Kaye, T.N. and R.J. Meinke
Publication_Date: 1992
Title:
Population monitoring and pollination biology of Snake River Goldenweed, Haplopappus radiatus
Geospatial_Data_Presentation_Form: report
Publication_Information:
Publication_Place: Salem, Oregon
Publisher: Oregon Department of Agriculture
Methodology_Citation:
Citation_Information:
Originator: Kaye, T.N. and M. Kirkland
Publication_Date: 1994
Title:
Cimicifuga elata: Status, habitat analysis, monitoring, inventory, and effects of timber management
Geospatial_Data_Presentation_Form: report
Publication_Information:
Publication_Place: Salem, Oregon
Publisher: Oregon Department of Agriculture
Methodology_Citation:
Citation_Information:
Originator: Kaye, T.N., K.L. Pendergrass, K. Finley, and J.B. Kauffman
Publication_Date: 2001
Title:
The effect of fire on the population viability of an endangered prairie plant
Geospatial_Data_Presentation_Form: Journal article
Series_Information:
Series_Name: Ecological Applications
Issue_Identification: in press
Process_Step:
Process_Description: Processing steps are described in Methodology
Process_Date: Unknown

Distribution_Information:
Distributor:
Contact_Information:
Contact_Organization_Primary:
Contact_Organization: USGS Forest & Rangeland Ecosystem Science Center
Contact_Address:
Address_Type: mailing and physical address
Address: 3200 SW Jefferson Way
City: Corvallis
State_or_Province: Oregon
Postal_Code: 973331
Contact_Voice_Telephone: (541) 750-7307
Contact_Facsimile_Telephone: (541) 758-7761
Resource_Description: <http://fresc.fsl.orst.edu/online/online_docs/kaye/appendix.pdf>
Distribution_Liability:
Although these data have been processed successfully on a computer system at the U.S. Geological Survey, no warranty expressed or implied is made regarding the accuracy or utility of the data on any other system or for general or scientific purposes, nor shall the act of distribution constitute any such warranty. This disclaimer applies both to individual use of the data and aggregate use with other data. It is strongly recommended that these data are directly acquired from a U.S. Geological Survey server, and not indirectly through other sources which may have changed the data in some way. It is also strongly recommended that careful attention be paid to the contents of the metadata file associated with these data. The U.S. Geological Survey shall not be held liable for improper or incorrect use of the data described and/or contained herein.
Standard_Order_Process:
Digital_Form:
Digital_Transfer_Information:
Format_Name: PDF
ASCII_File_Structure:
Case_Sensitive: false
Digital_Transfer_Option:
Online_Option:
Computer_Contact_Information:
Network_Address:
Network_Resource_Name: <http://fresc.fsl.orst.edu/online/online_docs/kaye/appendix.pdf>
Fees: None
Ordering_Instructions: Access on FRESC Website <http://fresc.orst.edu/>

Metadata_Reference_Information:
Metadata_Date: 20010726
Metadata_Review_Date: 20010816
Metadata_Future_Review_Date:
Metadata_Contact:
Contact_Information:
Contact_Person_Primary:
Contact_Person: Metadata Coordinator
Contact_Organization:
U.S. Geological Survey Forest and Rangeland Ecosystem Science Center
Contact_Address:
Address_Type: mailing and physical address
Address: 3200 SW Jefferson Way
City: Corvallis
State_or_Province: OR
Postal_Code: 97331
Contact_Voice_Telephone: 541-750-7343
Contact_Facsimile_Telephone: 541-758-7761
Contact_Electronic_Mail_Address: george_lienkaemper@usgs.gov
Metadata_Standard_Name:
FGDC Biological Data Profile of the Content Standard for Digital Geospatial Metadata
Metadata_Standard_Version: FGDC-STD-001-1998

Generated by mp version 2.6.2 on Tue Jan 15 10:56:04 2002