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Calibrating Abundance Indices of Red Back Salamanders at Harvard Forest 2014
Aaron
Ellison
Ahmed
Siddig
2015
Herpetologists and conservation biologists frequently use convenient and cost-effective, but less accurate, abundance indices (e.g. artificial cover boards or natural objects surveys) in lieu of more accurate but costly and destructive population size estimators to detect and monitor size, state, and trends of amphibian populations. Despite advantages and disadvantages to each approach, studies calibrating abundance indices so they can be used as reliable population estimators are rare. We calibrated indices based on surveys under artificial cover boards and natural objects with a more accurate estimator of population sizes of red back salamanders (Plethodon cinereus (Green)) in a New England forest. Plethodon cinereus is an ecologically significant indicator species of forest dynamics, and accurate calibration of these indices should increase their reliability for monitoring programs. Average density/m2, capture probability, relative density of both natural objects searches, and cover board observations of P. cinereus in 30 × 30-m plots at the Harvard Forest (Petersham, Massachusetts, USA) were similar in stands dominated by Tsuga canadensis (eastern hemlock) and deciduous hardwood species (predominantly Quercus rubra [red oak] and Acer rubrum [red maple]). Abundance indices based on both cover board and natural object surveys were able to be calibrated using density estimates of P. cinereus derived from depletion (removal) surveys. The cover board index underestimated the estimated density of P. cinereus by 40%, but the natural object survey underestimated it by about 55%. We conclude that when calibrated and used appropriately, abundance indices can provide cost-effective and reliable measures of P. cinereus abundance that may be used in conservation assessments and long-term monitoring of northeastern USA forests.
abundance
amphibians
hemlock
populations
salamanders
LTER controlled vocabulary
populations
disturbance
LTER core area
Harvard Forest
HFR
LTER
USA
HFR default
This dataset is released to the public under Creative Commons CC0 1.0 (No Rights Reserved). Please keep the dataset creators informed of any plans to use the dataset. Consultation with the original investigators is strongly encouraged. Publications and data products that make use of the dataset should include proper acknowledgement.
https://harvardforest.fas.harvard.edu/exist/apps/datasets/showData.html?id=hf246
Simes Tract (Harvard Forest)
-72.22
-72.21
+42.48
+42.47
215
300
meter
2014
2014
genus
Plethodon
species
cinereus
red back salamander
Information Manager
Harvard Forest
324 North Main Street
Petersham
MA
01366
USA
(978) 724-3302
hf-im@lists.fas.harvard.edu
Harvard Forest
324 North Main Street
Petersham
MA
01366
USA
(978) 724-3302
(978) 724-3595
https://harvardforest.fas.harvard.edu
Overview
Our calibration study involved four sequential steps that we can summarize in the following: (1) Identification of the study location, calibrated sampling methods and the study design. (2) Sampling salamanders using depletion method as population estimator, and both Artificial cover boards and natural object search a long transects as relative abundance indices. (3) Data analysis and abundance estimation by these three procedures mentioned in 2. (4) Establishment of the relationship between the depletion population estimator and cover board abundance index in one hand and natural object search on the other hand.
1. Study site and design
All measurements were taken within four 30 × 30-m plots were sited adjacent to the ongoing Harvard Forest Hemlock Removal Experiment. Two of these plots were located close to each other in stands dominated by eastern hemlock (Tsuga canadensis), and two plots were located in deciduous stands dominated by mixtures of oak (Quercus) and maple (Acer) species. The two hemlock plots were in a valley, whereas the two deciduous plots were on a drier ridge; the distance between the two stand types is ≈0.5 km. More detailed descriptions of the Simes Tract are given in Ellison et al. (2014).
We established the plots including the installation of the cover boards in May 2013 by placing them in contact with soil surface after removing the leaf litter. One year later we sampled red back salamanders in these four plots during two sampling sessions in July 2014: the first session ran from 14-17 July, and the second from 27-30 July. During each sampling session, we sampled red back salamanders in three parallel 30 × 1-m strip transects laid out within each of the four plots. Transects were separated from each other by 10 m. Along each of the two outer transects, we placed five cover boards (1 × 0.25 × 0.02 m rough-sawn T. canadensis planks), spaced 5-m from one another. Natural cover objects were sampled in all three transects, and depletion sampling also was done in all three transects. All plots, including natural objects on the forest floor, were left in similar conditions to those seen prior to sampling sessions.
2.1. Depletion sampling
It is a common way to estimating salamander’s population size and density based on the idea that the investigator is successively able to catching, counting and removing all individuals of the focal species from specific area (i.e. plot) during a relatively short sampling period(e.g. few days). Our depletion sampling procedure followed that developed by Hairston (1986), Petranka and Murray (2001), Bailey et al. (2004b). Every morning during each of the two four-day sampling sessions, we intensively searched for salamanders for ≈4 hours under dead wood, rocks, and leaf litter in each transect in each plot. All salamanders encountered were removed from the strip transect and placed into 0.7 × 0.3 × 0.15-m plastic baskets buried 5 m outside of the plots. The bottom 10 cm of each basket was filled with dirt and leaf litter to provide wet habitat and food; small holes were drilled in the bottoms to allow rain water to drain, and baskets were covered with mesh netting to provide shade and protection from predators. All salamanders collected remained in these baskets for the entire sampling session (up to 72 hours), and were released thereafter.
2.2. Cover-board sampling
At the same times that we did the depletion sampling and searched under natural cover objects, we also counted all salamanders observed under the cover boards. We lifted up each cover board and recorded the number of P. cinereus that we saw under it. Because two of the cover board transects spatially overlapped the removal transects, we treated the cover boards as “natural objects” along these transect, and so we also removed all salamanders encountered under these cover boards and placed them in the holding baskets.
3. Statistical analysis and abundance estimations
We estimated average capture probability and average population size of P. cinereus in each plot using Zippin’s regression method (Zippin, 1956 and 1958) as implemented in the Removal Sampling software, version 2.2.2.22 (Seaby and Henderson, 2007). In this method, the number of individuals captured (and removed from the sampling area) along each sampled transect each day was plotted as a function of the cumulative number of captures on previous days within the same transect. The estimated population size for each transect was defined as the point where the regression line intercepts the x-axis. Given this estimated population sizes for each transect (30-m2) we obtained the estimates of the population density/m2 by dividing the population size of each transect by the area of the transect (30-m2), as well as density/ha is calculated by multiplying the density/m2 by the area of the hectare(10000 m2). The average capture probability for each transect during the four days of depletion sampling was then estimated simultaneously as the slope of the regression line. We further estimated the average capture probability for P. cinereus in each habitat type as the average of the capture probabilities from all transects located in each habitat type.
A per-transect cover-board density index (salamanders/m2) was estimated as the average of the number of salamanders detected during each sampling session under all five cover boards along a transect, divided by the total area of the five cover boards (1.25 m2) placed along each transect. A per-transect index of natural-object density (salamanders/m2; excluding the cover boards) during each sampling session was estimated as the average of the number of salamanders captured only on the first day of sampling in each strip transect. By only using the first day of captures in estimating natural-object density, we intended to avoid effects of habitat disturbance (from searching) and ongoing removal sampling in the subsequent three days of each sampling session.
4. Abundance indices relationship to population density (Calibration)
We calibrated the two density indices (from cover boards and natural objects) by regressing them against the estimates of population size derived from the removal sampling. Exploratory analysis identified a single strong outlier point in the cover-board index; we repeated the regression analyses with the outlier present, removed, or replaced with the median of the cover board index.
hf246-01-calibrate-aco.csv
calibration aco
hf246-01-calibrate-aco.csv
2099
b6ca9ceffe232f008c612d3512195e71
1
\r\n
column
,
https://harvardforest.fas.harvard.edu/data/p24/hf246/hf246-01-calibrate-aco.csv
plot
plot number
plot number
`NA`

missing value
transect
transect number
transect number
`NA`

missing value
aco
artificial cover object number
artificial cover object number
`NA`

missing value
forest
type of forest at plot location
`hemlock`

hemlock stand
`hardwood`

hardwood stand
`NA`

missing value
session
sampling session
`1`

July 14-17, 2014
`2`

July 27-30, 2014
`NA`

missing value
day.1
number of salamanders observed under each cover board on the first
day
number
1
whole
`NA`

missing value
day.2
number of salamanders observed under each cover board on the second
day
number
1
whole
`NA`

missing value
day.3
number of salamanders observed under each cover board on the third
day
number
1
whole
`NA`

missing value
day.4
number of salamanders observed under each cover board on the fourth
day
number
1
whole
`NA`

missing value
80
hf246-02-calibrate-dep.csv
calibration depletion
hf246-02-calibrate-dep.csv
624
aa77d20852a7d1a6b9dfda2c4dc5a31c
1
\r\n
column
,
https://harvardforest.fas.harvard.edu/data/p24/hf246/hf246-02-calibrate-dep.csv
plot
plot number
plot number
`NA`

missing value
transect
transect number
transect number
`NA`

missing value
forest
type of forest at plot location
`Hemlock`

hemlock stand
`Hardwood`

hardwood stand
`NA`

missing value
session
sampling session
`1`

July 14-17, 2014
`2`

July 27-30, 2014
`NA`

missing value
day.1
number of salamanders captured and removed from transect on the first
day
number
1
whole
`NA`

missing value
day.2
number of salamanders captured and removed from transect on the second
day
number
1
whole
`NA`

missing value
day.3
number of salamanders captured and removed from transect on the third
day
number
1
whole
`NA`

missing value
day.4
number of salamanders captured and removed from transect on the fourth
day
number
1
whole
`NA`

missing value
24
hf246-03-calibrate-nos.csv
calibration nos
hf246-03-calibrate-nos.csv
456
a0a4e4d288ee784891e688b20341bfc1
1
\r\n
column
,
https://harvardforest.fas.harvard.edu/data/p24/hf246/hf246-03-calibrate-nos.csv
plot
plot number
plot number
`NA`

missing value
transect
transect number
transect number
`NA`

missing value
forest
type of forest at plot location
`hemlock`

hemlock stand
`hardwood`

hardwood stand
`NA`

missing value
session
sampling session
`1`

July 14-17, 2014
`2`

July 27-30, 2014
`NA`

missing value
count
number of salamanders detected within the area of the transect on the
first day of each session
number
1
whole
`NA`

missing value
24
hf246-04-regress-cb.csv
regression of abundance vs. cb index
hf246-04-regress-cb.csv
351
b1a54271daca70eb4bf620c05a5852a7
1
\r\n
column
,
https://harvardforest.fas.harvard.edu/data/p24/hf246/hf246-04-regress-cb.csv
plot
plot number
plot number
`NA`

missing value
transect
transect number
transect number
`NA`

missing value
forest
type of forest at plot location
`Hemlock`

hemlock stand
`Hardwood`

hardwood stand
`NA`

missing value
cb.index
estimated average salamanders count per ACO /
transect
number
0.1
real
`NA`

missing value
cb.density
relative density/ m2 computed based on average CB-index (i.e.0.25 m2)
multiplied by 4
numberPerMeterSquared
0.1
real
`NA`

missing value
nos.index
relative density of salamanders based on natural objects search in
30×1m-strip transects. Counts of salamanders per each transect was divided by the area of the
transect (30 m2) to estimate this index.
number
0.01
real
`NA`

missing value
pop.size
population size of salamanders per each transect as estimated by depletion
method
number
0.01
real
`NA`

missing value
density
estimated salamanders density based on the estimates of actual population
size/transect. It is population size per transect divided by the area of the transect
(30m2).
number
0.01
real
`NA`

missing value
8
hf246-05-regress-nos.csv
regression of abundance vs. nos index
hf246-05-regress-nos.csv
385
d99c1f65c6ed85fa9f9a3fd7ecbfeabd
1
\r\n
column
,
https://harvardforest.fas.harvard.edu/data/p24/hf246/hf246-05-regress-nos.csv
plot
plot number
plot number
`NA`

missing value
transect
transect number
transect number
`NA`

missing value
forest
type of forest at plot location
`Hemlock`

hemlock stand
`Hardwood`

hardwood stand
`NA`

missing value
pop.size
population size of salamanders per each transect as estimated by depletion
method
number
0.01
real
`NA`

missing value
density
estimated salamanders density based on the estimates of actual population
size/transect. It is population size per transect divided by the area of the transect
(30m2)
number
0.01
real
`NA`

missing value
nos.index
relative density of salamanders based on natural objects search in
30×1m-strip transects. Counts of salamanders per each transect was divided by the area of the
transect (30 m2) to estimate this index.
number
0.01
real
`NA`

missing value
12
completed
biodiversity
informatics
community
short-term measurement
modeling