Analysis of Atlantic Sea Scallop 

(Placopecten magellanicus) Fishery 

Impacts on the North Atlantic 

Population of Loggerhead Sea Turtles 

(Caretta caretta) 

U. S. DEPARTMENT OF COMMERCE 

National Oceanic and Atmospheric Administration 

National Marine Fisheries Service 

Northeast Fisheries Science Center 

Woods Hole, MA 

February 2008

NOAA Technical Memorandum NMFS-NE-207 
Recent Issues in This Series:

188. Northeast Regional Commercial Fishing Input-Output Model, by Scott R. Steinback and Eric M. Thunberg. NTIS Access. No. 

PB2007-104394. April 2006. v + 54 p., 2 figs, 15 tables. [Online publication only.] 

189. Essential Fish Habitat Source Document: Sea Scallop, Placopecten magellanicus, Life History and Habitat Characteristics. 

2nd ed. By Deborah R. Hart and Antonie S. Chute. September 2004. v + 21 p., 6 figs., 2 tables. NTIS Access. No. PB2005-104079. 

[Online publication only.] 

190. Essential Fish Habitat Source Document: Atlantic Cod, Gadus morhua, Life History and Habitat Characteristics. 2nd ed. By 

R. Gregory Lough. November 2004. vi + 94 p., 27 figs., 5 tables, 1 app. NTIS Access. No. PB2006-101528. [Online publication only.] 

191. Essential Fish Habitat Source Document: Northern Shortfin Squid, Illex illecebrosus, Life History and Habitat 

Characteristics. 2nd ed. By Lisa C. Hendrickson and Elizabeth M. Holmes. November 2004. v + 36 p., 13 figs., 1 table. NTIS Access. 

No. PB2005- 101437. [Online publication only.]

192. Essential Fish Habitat Source Document: Atlantic Herring, Clupea harengus, Life History and Habitat Characteristics. 2nd 

ed. By David K. Stevenson and Marcy L. Scott. July 2005. vi + 84 p., 40 figs., 7 tables. NTIS Access. No. PB2005-107567. [Online 

publication only.] 

193. Essential Fish Habitat Source Document: Longfin Inshore Squid, Loligo pealeii, Life History and Habitat Characteristics. 

2nd ed. By Larry D. Jacobson. August 2005. v + 42 p., 20 figs., 1 table. NTIS Access. No. PB2005-110684. [Online publication only.]

194. U.S. Atlantic and Gulf of Mexico Marine Mammal Stock Assessments -- 2005. By Gordon T. Waring, Elizabeth Josephson, 

Carol P. Fairfield, and Katherine Maze-Foley, eds. Dana Belden, Timothy V.N. Cole, Lance P. Garrison, Keith D. Mullin, Christopher 

Orphanides, Richard M. Pace III, Debra L. Palka, Marjorie C. Rossman, and Fredrick W. Wenzel, contribs. March 2006. v + 392 p., 45 

figs, 79 tables, 5 app., index. NTIS Access No. PB 2007-104395. 

195. A Large Marine Ecosystem Voluntary Environmental Management System Approach to Fisheries Practices. By Frank J. 

Gable. December 2005. v + 84 p., 38 figs., 10 tables. NTIS Access. No. PB____-______. 

196. Essential Fish Habitat Source Document: Haddock, Melanogrammus aeglefinus, Life History and Habitat Characteristics. 

2nd ed. By Jon K.T. Brodziak. December 2005. vi + 64 p., 27 figs., 2 tables. NTIS Access. No. PB2006-103439. [Online publication 

only.]

197. In preparation by author. 

198. Essential Fish Habitat Source Document: Bluefish, Pomatomus saltatrix, Life History and Habitat Characteristics. 2nd ed. 

By Jon K.T. Brodziak. December 2005. vi + 89 p., 48 figs., 5 tables, 1 app. NTIS Access. No. PB2006-103439. [Online publication 

only.]

199. Distribution and Abundance of Fish Eggs Collected during the GLOBEC Broad-Scale Georges Bank Surveys, 1995-1999. 

By John D. Sibunka, Donna L. Johnson, and Peter L. Berrien. August 2006. iv + 72 p., 28 figs., 1 table. NTIS Access. No. PB____-

______. [Online publication only.]

200. Essential Fish Habitat Source Document: Black Sea Bass, Centropristis striata, Life History and Habitat Characteristics (2nd 

ed. By Amy F. Drohan, John P. Manderson, and David B. Packer. February 2007. vi + 68 p., 33 figs., 2 tables. NTIS Access No. 

PB____-______. [Online publication only.]

201. U.S. Atlantic and Gulf of Mexico Marine Mammal Stock Assessments -- 2006. By Gordon T. Waring, Elizabeth Josephson, 

Carol P. Fairfield, and Katherine Maze-Foley, eds. Dana Belden, Timothy V.N. Cole, Lance P. Garrison, Keith D. Mullin, Christopher 

Orphanides, Richard M. Pace III, Debra L. Palka, Marjorie C. Rossman, and Fredrick W. Wenzel, contribs. March 2007. vi + 378 p., 92 

figs, 84 tables, 5 app., index. NTIS Access No. PB____-______. 

202. Evaluation of Northern Right Whale Ship Strike Reduction Measures in the Great South Channel of Massachusetts. By RL 

Merrick and TVN Cole. March 2007. NTIS Access No. PB____-______. 

203. Essential fish habitat source document: Spiny dogfish, Squalus acanthias, life history and habitat characteristics, 2nd 

edition. By LL Stehlik. December 2007. NTIS Access No. PB____-______. 

204. An Evaluation of the Northeast Region’s Study Fleet pilot program and Electronic Logbook System: Phases I and II. By 

Michael C. Palmer, Susan E. Wigley, John J. Hoey, and Joan E. Palmer. December 2007. NTIS Access No. PB____-______. 

205. In preparation by author. 

206. Growth of Black Sea Bass (Centropristis striata) in Recirculating Aquaculture Systems. By Dean M. Perry, David A. Nelson, 

Dylan H. Redman, Stephan Metzler, and Robin Katersky. October 2007. NTIS Access No. PB____-______. 
Analysis of Atlantic Sea Scallop 

(Placopecten magellanicus) Fishery Impacts 

on the North Atlantic Population of 

Loggerhead Sea Turtles (Caretta caretta) 

Richard Merrick and Heather Haas 

National Marine Fisheries Service, 166 Water Street, Woods Hole, MA 02543

 

U.S. DEPARTMENT OF COMMERCE 

Carlos M. Gutierrez, Secretary 

National Oceanic and Atmospheric Administration 

Vice Admiral Conrad C. Lautenbacher, Jr., USN (ret.), Administrator 

National Marine Fisheries Service 

James W. Balsiger, Acting Assistant Administrator for Fisheries 

Northeast Fisheries Science Center 

Woods Hole 

February 2008

NOAA Technical Memorandum NMFS-NE-207 

This series represents a secondary level of scientific publishing. All issues employ thorough internal 

scientific review; some issues employ external scientific review. Reviews are transparent collegial 

reviews, not anonymous peer reviews. All issues may be cited in formal scientific communications. 
 

ii

Editorial Notes 

Species Names: The NEFSC Editorial Office’s policy on the use of species names in all 

technical communications is generally to follow the American Fisheries Society’s lists of 

scientific and common names for fishes, mollusks, and decapod crustaceans and to follow the 

Society for Marine Mammalogy's guidance on scientific and common names for marine 

mammals. Exceptions to this policy occur when there are subsequent compelling revisions in the 

classifications of species, resulting in changes in the names of species. 

Statistical Terms: The NEFSC Editorial Office’s policy on the use of statistical terms in all 

technical communications is generally to follow the International Standards Organization’s 

handbook of statistical methods. 

Internet Availability: This issue of the NOAA Technical Memorandum NMFS-NE series is 

being as a paper and Web document in HTML (and thus searchable) and PDF formats and can be 

accessed at: http://www.nefsc.noaa.gov/nefsc/publications/. 
 

iii

TABLE OF CONTENTS

Abstract.......................................................................................................................................... iv 

Introduction..................................................................................................................................... 1 

Methods........................................................................................................................................... 2 

Data............................................................................................................................................. 2 

Population trend data .............................................................................................................. 2 

Current abundance data........................................................................................................... 2 

Fishery mortality data ............................................................................................................. 3 

Model .......................................................................................................................................... 5 

Modeling Steps ........................................................................................................................... 6 

Evaluation of Results .................................................................................................................. 7 

Results............................................................................................................................................. 7 

Population Trends to Present ...................................................................................................... 7 

Viability Analyses....................................................................................................................... 8 

Model Sensitivity........................................................................................................................ 8 

Discussion....................................................................................................................................... 9 

Acknowledgments......................................................................................................................... 11 

References Cited ........................................................................................................................... 20 
 

iv

ABSTRACT

An estimated 619 loggerhead turtles of various age and sex classes were taken annually 

during 1989-2005 in all components of the US Atlantic sea scallop (Placopecten magellanicus) 

fishery. We provide here a quantitative assessment of the potential for these takes to jeopardize 

the continued existence of the US Atlantic Ocean population of loggerhead sea turtles (Caretta 

caretta). A population viability analysis (PVA) was used to estimate quasi-extinction 

likelihoods under conditions with and without fishery effects. This PVA used US index nesting 

beach data for 1989-2005 to estimate the loggerhead population trend μ (mean growth rate) and 

variance σ

2

. The starting population (N0) for the exercise was the sum of nesting females 

estimated from the 2005 nest count in the North Carolina to Florida area. The base model (with 

fishery bycatch) was developed by using estimates of μ (-0.022), σ

2 (0.012), N0 (34,881) and a 

quasi-extinction threshold of 250 adult females. Quasi-extinction likelihoods were bootstrapped 

(1000 iterations) under baseline conditions to derive confidence intervals. The μ for each 

bootstrap iteration was drawn from a normally distributed random sampling of μ values lying 

within the 95% confidence interval around the original μ. The model was then rerun with the 

estimated annual fishery mortality of adult females (102 turtles) added back into the population, 

thus changing the trend (μ = -0.019, σ

2

 = 0.012, and N0 = 34,881). Results of the two models 

were similar; the quasi-extinction probabilities were zero at 25, 50, and 75 years, and 0.01 at 100 

years for both analyses. Median times to quasi-extinction were 207 years versus 240 years, and 

the number of bootstrap simulations with extinction probabilities greater than 0.05 in 100 years 

was 258 and 178, respectively. These results suggest that the annual take of loggerhead sea 

turtles in the US fisheries for Atlantic sea scallops, though detectable, does not significantly 

change the calculated risk of extinction of the population of adult female Western North Atlantic 

loggerheads over the next 100 years. 
INTRODUCTION

Loggerhead sea turtles (Caretta caretta) are incidentally captured in US dredge and trawl 

fisheries for Atlantic sea scallops (Placopecten magellanicus) in the US Mid-Atlantic region. 

Increased federal observer coverage of these fisheries allowed the National Marine Fisheries 

Service (NMFS) to estimate the annual bycatch of loggerhead turtles in the fisheries through 

2005 (Murray 2004a, 2004b, 2005, 2007). Recent observer reports document takes through 

2007. As loggerhead turtles are a threatened species under the US Endangered Species Act 

(ESA), NMFS, under Section 7 of the ESA, must ensure that continuation of the sea scallop 

fisheries is not likely to jeopardize the continued existence of the species. 

 Impacts of US fisheries (e.g., Atlantic sea scallop, Mid-Atlantic bottom trawl, pelagic 

longline, and Gulf of Mexico/Southern Atlantic commercial shrimp) on the western North 

Atlantic loggerhead sea turtle population have been analyzed by Southeast Fisheries Science 

Center (SEFSC) staff and the loggerhead sea Turtle Expert Working Group (TEWG 1998, 2000; 

SEFSC 2001; Epperly et al. 2002). However, reduced loggerhead nesting on southeastern US 

beaches suggests these analyses require updating. The TEWG is currently working on a 

reanalysis, but the limited data available on current population parameters (e.g., stage specific 

survival) suggest that the previous demographic models may be difficult to revise. 

 We provide here an alternative quantitative approach to the assessment of the risk the US 

Atlantic sea scallop fisheries have of jeopardizing the continued existence of the western North 

Atlantic Ocean populations of loggerhead sea turtles. This approach is simpler than previously 

used for western North Atlantic (WNA) loggerheads and is similar to that used by Snover (2005) 

in her analysis of the impact of the Western Pacific Pelagics Fisheries on several Pacific sea 

turtle species. We use a population viability analysis (PVA) to estimate quasi-extinction 

likelihoods under conditions with and without fishery effects. The PVA is count-based (Dennis 

et al. 1991; Morris et al. 1999; Holmes 2001; Morris and Doak 2002; Snover 2005) which will 

allow the use of the only relatively complete and available population time series—index nesting 

beach1

 counts for 1989-2005. As such, the analyses focus on the viability of the adult female 

portion of the population and should not be considered to model viability of the entire 

population. 

 We first present the PVA results under baseline conditions by using the rate of change of 

the adult female population (which implicitly includes the mortalities from the scallop and other 

fisheries) and the 2005 count of adult females estimated from all beaches in the Southeast based 

on an extrapolation from nest counts. We then adjust the rate of change by adding back the 

fisheries take and rerunning the PVA. The results of these two analyses are then compared by 

using the probability of quasi-extinction at 100 years to assess the impact of the takes in the 

Atlantic sea scallop fisheries. 

 At the outset, we point out three caveats to the interpretation of these analyses. First, the 

current negative nesting beach trends are at odds with some in-water survey results (e.g., Epperly 

et al. 2007). Secondly, the current negative trend in adult female abundance has likely been 

 

1

 Index beaches are a limited series of beaches which are regularly monitored for nesting activity. In Florida, the 

Index Nesting Beach Survey (INBS) has coordinated a detailed monitoring program since 1989 to measure seasonal 

productivity, allowing comparisons between beaches and between years. In Florida, 33 beaches (of 190 surveyed 

beaches) are included in the INBS program. Similar programs exist in states further north. 
 

2

influenced by mortality events that have occurred over several decades. As such, a model based 

on current nesting beach trends may overestimate the effect of current takes on the likelihood of 

extinction for the population. Finally, we stress that our analyses should not be used to assess 

the likely fate of the population but should only be used to assess the impact of the fisheries for 

Atlantic sea scallops on the population trajectory of adult female loggerhead sea turtles. A 

thorough review of loggerhead population trends is provided by Witherington et al. (2006, in 

review). 

METHODS

Data 

Population trend data 

A time series of population counts (or some index of the population) was needed through 

2005 to estimate the population trend for the PVA. The time series needed to be longer than 10 

years for the PVA to be more than marginally useful (Morris et al. 1999; Morris and Doak 2002). 

 Loggerhead nest counts (a proxy for the adult female population) are available for 

southeastern US index nesting beaches from 1989 to 2005 for the Northern (NC, SC, and GA) 

and Peninsular Florida subpopulations (NMFS in review, FWRI 2007). These are the 

subpopulations with the greatest nesting populations. Two other southeastern United States 

subpopulations have index beach nest counts available from 1996 (Dry Tortugas FL) and 1998 

(Northern Gulf [AL, FL]) onwards (NMFS in review). These are the two smallest 

subpopulations, and since at least 1996 they have constituted a small fraction of the population 

(e.g., in 2005 they accounted for only 3% of the total number of index beach nests). Because 

nest counts were available for only a relatively brief period, these two subpopulations were 

excluded from the trend analysis for 1989-2005. Note that we did include the nest counts for all 

four subpopulations as part of a supporting analysis for the 1996-2005 period. Finally, these 

count data were used directly, without any adjustments for remigration2 or nests per female, to 

determine the population trend. 

Current abundance data 

An estimate of adult female abundance in 2005 was necessary for use as the starting point 

for the PVA. The 2005 estimate of adult female abundance was derived by first summing nest 

counts from all beaches surveyed in the southeastern United States, including all beaches 

surveyed in 2005 in NC, SC, GA, FL, and AL (NMFS in review, FWRI 2007, SCDNR 2007). 

Only index beach nests counts were available for the Dry Tortugas and Northern Gulf 

subpopulations, so the total nest count is biased low. We then adjusted the sum to estimate adult 

females: 

NAF = (Number of nests/Nests per female) * Remigration interval 

 

2

 Remigration is used here to mean the number of years between visits by adult females to nesting beaches and is 

not to be confused with the repeat visits within a single year which are included in the nests per female estimate. 
 

3

Use of a constant value for nests per female and remigration interval is problematic as 

both parameters vary to some degree. For example, limited food resources can lead to decreased 

reproductive fitness because of natural and human driven fluctuations in prey availability. 

Moreover, if the age structure of the population changes, the number of nests per female will 

change. The available datasets do not characterize this variability, nor is it known whether such 

variability is random or associated with environmental change. Because of these uncertainties, 

we generally used conservative parameter values. 

 Estimates of nests per female vary widely, in part because of observational issues. 

Estimates adjusted for missed nesting suggest the mean number of nests per female per season in 

US waters ranges from 2.8 to 4.2 (Frazer and Richardson 1985; Schroeder et al. 2003). We used 

4.2 nests per female. 

 Published estimates for the average remigration intervals of WNA loggerhead sea turtles 

on US beaches vary from 2.5 to 2.7 years (Richardson et al. 1978; Bjorndal et al. 1983; 

Schroeder et al. 2003). We used the 2.5 year remigration estimate. 

Fishery mortality data 

Estimates of loggerhead bycatch in the US Atlantic sea scallop fisheries are available for 

2003-2005 for scallop dredge gear and for 2004-2005 for scallop trawl gear (Murray 2004a, 

2004b, 2005, 2007). There is a wide range amongst the annual values, and two approaches for 

deriving an estimate for our model were considered. One approach was based on using the mean 

annual sea scallop dredge fishery bycatch for 2003-2005 ([749+180+0]/3=310; Murray 2004b, 

2007) added to the midpoint of the range of estimated sea scallop trawl fishery bycatch from six 

bycatch estimates for 2004-2005 (136 turtles; Murray 2007) as the estimate of average annual 

total loggerhead sea turtles caught in the sea scallop fisheries (446 turtles). An additional 20 

loggerheads were estimated to have been caught in groundfish bottom trawl fisheries where sea 

scallops were the primary catch (Murray 2006). Summing across fisheries suggests that the 

annual loggerhead bycatch in sea scallop related fisheries in 2004-2005 might be 466 animals. 

 The second approach used the take estimates in the Atlantic Sea Scallop Fishery 

Management Plan (FMP) Biological Opinion. This included only the 2003-2004 sea scallop 

dredge fishery bycatch (biennially 929 loggerhead sea turtles) added to one of the sea scallop 

trawl fishery bycatch estimates (268 loggerhead sea turtles biennially) and the 20 turtles 

estimated to be taken annually in groundfish bottom trawls for an average annual bycatch of 619 

loggerhead sea turtles in the fishery. 

 We used the value of 619 loggerhead sea turtles as our estimate of the annual bycatch in 

the sea scallop fisheries of loggerhead sea turtles of various age and sex classes. 

 This total loggerhead sea turtle bycatch estimate (NB=619 turtles) then needed to be 

adjusted downward to estimate the annual mortality of adult female loggerheads (NAF) associated 

with the US sea scallop fisheries: 

NAF = (NB*FUS *FM *FM-F *FL) + (NB*FUS *[1-FM]*FIM-F * FIM-R *FL) 

where: 

 FUS = proportion of the bycatch from the US population 

 FM = proportion of bycatch mature 
 

4

 FM-F = proportion of the adult bycatch assumed to be female 

FIM-F = proportion of the immature bycatch assumed to be female 

 FIM-R = relative reproductive value of juvenile neritic turtles 

FL = proportion of the bycatch considered as lethal takes 

Again, where there was a range of parameter values, we selected the value that generated the 

greatest impact by the sea scallop fisheries on the loggerhead population: 

1. FUS - Genetic samples taken from loggerhead sea turtles captured in the sea scallop 

fisheries indicated that 88-93% of the animals are from the US nesting population (Haas 

et al. in review). This is comparable to the ~92% reported by Bass et al. (2004) for the 

Albemarle-Pamlico Sounds area of NC. We used a value of 93%. 

2. FM - Loggerheads captured in both gear types are expected to be of the same age classes. 

Loggerhead sea turtles observed bycaught in sea scallop fisheries ranged in size from 62 

cm to 107 cm curved carapace length (CCL)(mean = 79.2 cm CCL, SD = 11.6, NE 

Fishery Observer Program database). The cutoff between sexually immature and mature 

loggerhead sea turtles appears is in the range of 87 to 100 cm CCL (NMFS in review; 

SEFSC 2001). CCL data were available for 42 turtles taken in the fishery; 35 (83.3%) 

were less than 87 cm CCL. As such, we used 0.833 as the proportion of immatures taken 

in the fisheries. 

3. FM-F and FIM-F – There are few data available on the sex classes of loggerheads bycaught 

in the sea scallop fisheries. We, therefore, used data available from loggerhead captures 

and strandings. These data suggest that the mature and immature sex ratio in Northeast 

waters is approximately two females per male (TEWG 2000). 

4. FIM-R – Estimated bycatch of immature loggerheads was adjusted to account for the 

natural mortality expected prior to their recruitment as breeding adults. Wallace et al. (in 

press) present estimates in the range of 0.28 to 0.32 for the relative reproductive value of 

the neritic juvenile stage of loggerhead sea turtles found stranded along the US Atlantic 

coast (mean CCL = 78.5, SD = 16.6). Given the similarity in size of these loggerheads to 

those taken in the sea scallop fishery (mean CCL = 79.2, SD = 11.6), it appears 

reasonable to use this estimation of reproductive value for immature juvenile turtles taken 

in the sea scallop fishery. We, therefore, used 0.32 as the estimate for juvenile 

reproductive value. 

5. FL - Observer reports from the 2003-2005 fisheries suggest that the percentage of 

loggerhead sea turtles released alive and uninjured was 22.7-25% for scallop dredge gear 

and 100% for trawl gear (Murray 2004a, 2004b, 2005, 2007). This compares to the 36% 

and 88.5% used in the Atlantic Sea Scallop FMP Biological Opinion. We, therefore, 

used 0.227 and 0.885 for dredge and trawl gear, respectively. 

Because of the differences in loggerhead captures in the trawl and dredge fisheries, the number 

of adult female mortalities was estimated separately for each fishery and then combined. 
 

5

 Together this series of adjustments provides an estimate of the annual mortality (in 

numbers) of US adult female loggerheads caused by the bycatch in the US Atlantic sea scallop 

fisheries. 

 

Model 

The Dennis Model is a density-independent model of population growth, which uses a 

diffusion approximation to compute the probability of quasi-extinction (i.e., reaching a low 

threshold population size) in a randomly varying environment: 

Nt+1 = Ntλt

Application of the model requires that two key parameter values be estimated to make inferences 

regarding population growth rates and quasi-extinction risks: 

μ – the arithmetic mean of the log population growth rate 

σ

2

 – variance of the log population growth rate 

Holmes (2001) suggests the use of running sums as a means of reducing bias associated with 

sampling error and stage-specific counts. We calculated running sums as: 

Rj = Ni + Ni+1

where j=1,2,3 ... (q-1), q is the number of censuses in dataset, N represents the population size, 

and Rj represents the population size at time j from the running sums. Without using the running 

sums approach (1 yr intervals), the trend was -0.0063 and the variance was 0.038. We evaluated 

running sums of 2 yr, 3 yr, and 4 yr to calculate the annual estimate of Rj and found that the 3 

and 4 yr running sums produced the same rate of change (-0.0216), which was slightly different 

from the 2 yr interval (-0.0220). With the smaller variance in the trend for the 3 and 4 yr running 

sums (0.006 and 0.003, respectively), the result would be that a 3 or 4 yr interval would lead to 

reduced probabilities of quasi-extinction in 100 yrs. Following our rule of using conservative 

parameter values, we decided to use a 2 yr interval for the final analysis. 

 Then μ was calculated as: 

μ = (∑log(Rj+1/Rj )/t 

Similarly, σ

2 is calculated as the variance over the series of log (Ri+1/Ri) values. The μ and σ2

 are 

then used to estimate r (the instantaneous rate of change) and λ (Dennis et al. 1991): 

r = μ + σ

2

/2 

λ = e (r)

Estimation of the extinction risk requires a population size at extinction (Next). The 

population size at extinction can assume several values, with 0 equal to the true extinction. 

Rather then focusing entirely on total extinction (Next = 0), the concept of quasi-extinction risk 

has been developed (Ginzburg et al. 1982), where quasi-extinction risk is the probability that a 
 

6

population will fall below a given threshold (Next > 0). There is no generally agreed upon level 

for quasi-extinction, though it is commonly considered to be a threshold population size below 

which the population would be critically endangered or effectively extinct. For large vertebrates, 

a variety of numerical values have been considered for this threshold (e.g., from 20 to 500). We 

considered using either 50 or 250 adult females as our estimate of quasi-extinction. Our reasons 

for considering fifty animals were: (1) there is general consensus in the conservation genetics 

community that large vertebrate populations cannot fall below 50 breeding animals and still 

maintain genetic integrity (Shaffer 1981; Franklin 1980), (2) the International Union for 

Conservation of Nature (IUCN)(2008) considers this to be one of the two threshold numerical 

values for a “critically endangered” population category, and (3) to provide comparability with 

the value used in the 2004 Pacific sea turtle bycatch PVA prepared by Snover (2005). IUCN 

uses 250 mature animals as an alternative threshold value for “critically endangered” populations 

when there is evidence of a population decline. Given the apparent decline in nesting in the 

southeastern United States, it appears reasonable to use 250 as our threshold value for quasiextinction. The IUCN includes all mature animals in this value and not just adult females, so 

using 250 adult females as the threshold provides a doubly conservative threshold. 

 Morris and Doak (2002) describe the probability of reaching a quasi-extinction threshold 

(Next) by using the following function: 

g(t| μ, σ

2

, d) = ⎥

⎦

⎤ ⎢

⎣

⎡− +

t

d t

t

d

2

2

2 3 2

( ) exp

2 σ

μ

πσ

with d = log(N0/Next), and N0 is the population size at the beginning of the analysis period. To 

calculate the total probability of reaching Next at some future time T, the cumulative distribution 

function (which is the preceding function integrated from t = 0 to T) is applied: 

G(T| μ, σ

2

, d) = ⎥

⎥

⎦

⎤

⎢

⎢

⎣

⎡

− − + Φ ⎥

⎥

⎦

⎤

⎢

⎢

⎣

⎡

− + Φ

⎥

⎥

⎥

⎥

⎦

⎤

⎢

⎢

⎢

⎢

⎣

⎡

−

∧

∧

∧

∧

∧

∧

T

d T

T

d d T

2 2

2

2

exp

σ

μ

σ

μ

σ

μ

where Ф(z) is the standard normal cumulative distribution function (Morris and Doak 2002). 

 Morris and Doak (2002) outlined an approach for deriving the quasi-extinction time 

cumulative distribution function confidence intervals by using bootstrap estimation procedures. 

We used a similar approach, sampling from a random distribution drawn from within the 95% 

confidence interval for μ and σ

2

 and replicated 1000 times to estimate the confidence intervals 

around the cumulative probability of reaching Next at some future time T. 

Modeling Steps 

The base model (with fisheries bycatch) was run over a 1,000 yr period with the estimates 

of μ, σ

2

, N0 beginning in 2005 and quasi-extinction threshold of 250 adult female loggerheads 

(Dennis et al. 1991; Holmes 2001; Morris and Doak 2002; Snover 2005). The 1,000 year time 

horizon was necessary so that we could determine the median time to extinction. Quasiextinction likelihoods were then bootstrapped under baseline conditions to derive confidence 
 

7

intervals. The μ for each bootstrap iteration was drawn from a normally distributed random 

sampling of μ values lying within the 95% confidence interval around the original μ. 

 The model was modified to add back in the annual loggerhead bycatch in the Atlantic sea 

scallop fisheries. First, we adjusted the annual estimated bycatch in the fisheries (dredge and 

trawl) of loggerhead sea turtles for all age and sex classes to derive an estimate of total adult 

females removed from the population. We then calculated the rate of adult female removals for 

2005 by dividing the bycatch by the total adult female population in 2005. This rate was then 

added into the population instantaneous growth rate (r) for each year from 1989 to 2005, and a 

revised μ and σ

2 was calculated. The model (without fishery bycatch) was then run with the 

revised estimates of μ, σ

2

, and N0. We bootstrapped quasi-extinction likelihoods under the new 

model’s conditions to derive confidence intervals. 

Evaluation of Results 

The primary metric we used to compare the results of the two PVAs (with and without 

the fishery mortalities) was the cumulative probability of quasi-extinction at 100 years (based on 

recommendations on acceptable risk of extinction in DeMaster et al. 2004). Secondary metrics 

included the number of bootstrap replicates with a probability of extinction > 0.05 in 100 years 

and the median times to extinction3. We analyzed the sensitivity of the 1989-2005 model to 

changes in the population trend by comparison with the trend from 1996-2005. We also 

compared extinction probabilities at take levels that were two and ten times the documented 

levels of takes in the sea scallop fisheries. 

RESULTS

Population Trends to Present 

Loggerhead nest counts from the Northern and Peninsular subpopulations were summed 

(Fig. 1) and analyzed to develop the annual rates (λ) of population change for 1989-2005 (Table 

1). The trend (μ = -0.022, σ

2

 = 0.012, Table 2) for 1989-2005 for the US Atlantic Ocean 

loggerhead adult female population suggests the adult female population is declining. 

 We used an estimate of 58,6024

 nests in 2005 in the southeastern United States (North 

Carolina to Alabama). This produced an estimate of 34,881 adult females when adjusted for 

nests per female (4.2 nests per female) and remigration interval (2.5 years). 

 The annual sea scallop fisheries bycatch mortality of adult female loggerheads was 

estimated to be 102 turtles (97 in the dredge fishery and 5 in the trawl fisheries). This estimate 

was derived from the total annual take of 619 loggerheads prorated for area of origin (0.930 from 

United States), maturity (0.833 immature), female proportion (0.67), reproductive value of 

juveniles (0.32), and fishery specific mortality (dredge = 0.773 and trawl = 0.115). 

 Given the 2005 population estimate of 34,881 adult females and a fishery-induced 

mortality of 102 adult females per year, the rate of adult female removals in the sea scallop 

 

3

 The time when the quasi-extinction probability is 0.50 

4

 This includes 2005 counts for all beaches in the Northern (NC = 560, SC = 4,233, GA = 1,145 nests) and 

Peninsular Florida (51,636 nests) subpopulations and index beaches in the Dry Tortugas (159 nests) and Northern 

Gulf (869 nests) subpopulations (NMFS in review; FWRI 2007; SCDNR 2007). 
 

8

fishery was 0.0029 in 2005. These mortalities were added back into the population to produce a 

revised 1989-2005 μ of -0.019 (σ

2

 = 0.012, Table 2). 

Viability Analyses 

Using the 1989-2005 model, the risk of quasi-extinction (Next = 250 adult females) at 100 

years was 0.01 (Table 2, Fig. 2) with a median time to extinction of 207 years (Table 2). Over 

1000 iterations of the model, 258 produced a probability of extinction at 100 years greater than 

0.05. 

 Adding the Atlantic sea scallop fisheries-related loggerhead mortalities back into the 

population had only a small effect on population trajectory and extinction probabilities. The μ

was -0.022 and -0.019 for the analyses with and without the fishery takes. The risk of quasiextinction at 100 years remained 0.01 (Table 2, Fig. 3). The median time to extinction grew to 

240 years (Table 2). Over 1000 iterations of the model, 178 produced a probability of extinction 

at 100 years greater than 0.05. 

 Results of the two analyses were similar (Table 2, Fig. 4). Both had quasi-extinction 

probabilities of zero (0) at 25, 50, and 75 and a probability of 0.01 at 100 years. Median times to 

quasi-extinction were similar (207 years versus 240 years). The number of simulations with 

extinction probabilities at 100 years greater than 0.05 was 258 and 178, respectively. 

Model Sensitivity 

An incorrect estimate of the population trend would significantly affect the model results. 

Therefore, we repeated this analysis with just the 1996-2005 time series. While this would 

generally be considered to be too short a time series for analysis, it does provide some insight 

into the capability of the model to detect risk of extinctions. 

 Loggerhead nest counts from all four subpopulations were summed (Table 3) and 

analyzed to develop the annual rates (λ) of population change for 1996-2005 (Table 4). The 

trend (μ = -0.049, σ

2

 = 0.011, Table 2) for 1996-2005 for the US Atlantic Ocean loggerhead adult 

female population suggests even more strongly than the 1989-2005 analysis that the adult female 

population is declining. Again with the 2005 population estimate of 34,881 adult females and a 

fishery-induced mortality of 102 adult females per year, the rate of adult female removals in the 

sea scallop fishery was 0.0029 in 2005. These mortalities were added back into the population to 

produce a revised 1996-2005 μ of -0.046 (σ

2

 = 0.011, Table 4). 

 There was little difference between the 1996-2005 analyses with and without the sea 

scallop fisheries mortalities (Tables 4, Fig. 5). The population trend remains similar; μ equals 

0.049 and 0.046 for the two analyses. Cumulative probabilities of extinction are identical up 

until approximately the 75th year, and the median times to extinction were very similar for both 

1996-2005 models (i.e., 98 versus 102 years). The number of simulations with extinction 

probabilities at 100 years greater than 0.05 was 940 and 922, respectively. 

 We also evaluated the model’s sensitivity to changes in fishery mortality rates. Given 

that the 1989-2005 model showed probabilities of extinction at 100 years equal to zero for both 

the original model and the model with takes added back in, it was necessary to use the 1996-

2005 model for this evaluation. We compared the results of adding the loggerhead mortalities 

caused by the Atlantic sea scallop fisheries (102 adult females) with adding back in mortalities 

that were two and ten times greater than that observed in the sea scallop fisheries (Fig. 6). 
 

9

Ultimately, it appears that the probability of extinction at 100 years would be reduced to zero if 

ten times the number of adult females estimated to be taken by the Atlantic sea scallop fisheries 

were added back to the population. 

DISCUSSION

These results suggest that mortalities of loggerhead sea turtles in the US Atlantic sea 

scallop dredge and trawl fisheries are detectable but have a relatively small effect on the 

trajectory of the adult female components of the WNA loggerhead sea turtles over the next 100 

years. The 1989-2005 population trends, with and without the mortalities, were not significantly 

different, and the probability of reaching the quasi-extinction threshold (250 adult females) under 

both scenarios was 0.01. Median times to extinction for both were greater than 200 years. The 

only obvious difference was in the number of bootstrap simulations with a probability of 

extinction > 0.05 in 100 years. 

 The relatively large population size of adult females (34,881), the relatively small 

negative trend in the adult female population over 1989-2005 (r = -0.022 per year), and the 

number of adult female mortalities in the fisheries (102 per year) all contribute to the lack of 

effect. This lack of impact occurred despite the use, wherever possible, of values which 

generated the greatest consequence of the sea scallop fisheries takes of loggerheads. If less 

stringent values had been used, the effect would have been less. Patterson and Murray (2008) 

provide commentary on the effect that application of the precautionary principle to a PVA may 

have on “robust inference” and defensible policy. 

 Even a model as simple as the Dennis model is sensitive to parameter values and data 

inputs. Values calculated or selected for μ, Next, and σ

2

 were all influential. With respect to μ, 

we found that relatively small changes in the population trend produced profound changes in the 

probability of quasi-extinction at 100 years. For example, doubling the rate of decline in the 

base model (from -0.022 to -0.049) greatly increased the probability of extinction at 100 years 

from 0.01 to 0.54. In contrast, the level of bycatch mortality value removed from the population 

would need to be much greater than that observed in the sea scallop fisheries to have a major 

effect on the population trajectory. The comparison of the effect of different background 

mortalities (Fig. 6) suggests that up to ten times the level of loggerhead mortality in the sea 

scallop fisheries needs to be removed to stabilize the population. This small effect is important in 

that it suggests the relatively steep declining trend for 1996-2005 is being driven by some other, 

larger source of mortality. 

 Recognizing the influence of the population trend to the analysis, it is important to point 

out our assumption that the nesting beach data used in this analysis were representative of trends 

of the US loggerhead population. This was a practical decision; only the index beaches are 

counted annually in a systematic fashion. However, there is a risk in this assumption. We noted 

earlier the problem of juvenile in-water counts being at odds with the nesting trends. There is 

also some concern about the representativeness of the nest counts. If loggerhead nesting shifts 

systematically between years (either inside or outside of the index beach areas), then trends in 

the index nesting beach data may not represent the overall trend. For example, if loggerhead 

nesting is becoming more aggregated at the index sites (because of issues such as habitat 

protection), then the estimates may be biased high. Alternatively, if turtles nest outside of the 

time period (for example, earlier nesting caused by warmer climate conditions), then the index 

site estimates would be biased low. Work underway by the loggerhead TEWG and Florida’s 
 

10

Fish and Wildlife Research Institute will provide a substantive review of these trends. Our focus 

here was with evaluating the impact of the bycatch mortality in the Atlantic sea scallop fisheries 

on the future of the loggerhead population, and the impact of such biases on our analysis are 

likely immaterial. These biases could, however, significantly influence an analysis of population 

status and perhaps result in inappropriate management decisions. 

 The quasi-extinction value selected was also influential, but not as dramatically as the 

population trend. We evaluated Next values of 50 and 250 adult females. With the 1989-2005 

base model, the probabilities of extinction at 100 years were 0.00 and 0.01 for 50 and 250 

animals, respectively. Larger differences were observed in the 1996-2005 base model, where the 

values were 0.07 and 0.42 respectively. The latter, larger effect is likely due to the increased 

negative population trend. We also considered using the percent of decline approach suggested 

by Snover and Heppell (in press). We estimated the probability of reaching 50% of the current 

population size. Although risks of reaching the threshold were much higher (0.97 and 0.95 in 

100 years) than with the 50 or 250 animal threshold, there were no significant differences 

between the base model and the model with takes added back in. Ultimately, we decided to use 

an absolute value of Next = 250 adult females largely because this analysis was designed to 

evaluate the risk of extinction resulting from mortalities in the scallop fisheries, and 250 animals 

better represents a threshold extinction value than does 50% of the current population size (Next = 

17,441 adult females). 

 The model is also sensitive to changes in the variance; as the variance increases, the 

probability of extinction at any point in time increases, and as the variance decreases, 

probabilities of extinction decrease. Here it was assumed that the variance in the population 

trend is largely the same with and without the sea scallop fishery takes. Violations of this 

assumption would not change the interpretation of the sea scallop fisheries impacts, unless the 

take estimates were much higher relative to the population size and the variance in the takes was 

large. 

 However, the largest issue with variance was not the influence on the outcome but the 

difficulty of providing meaningful tests of significance with large confidence intervals. Using 

bootstrap techniques produced much tighter confidence intervals, but trajectories would need to 

vary considerably to find statistical differences. 

 Finally, this analysis was undertaken to provide a simple evaluation of the effect that 

loggerhead bycatch in the Atlantic sea scallop fisheries could have on the future viability of the 

WNA loggerhead population. It was not designed to and should not be used to evaluate 

population status. For example, here we implicitly assume that adult female recruitment will not 

change in the future. This is a particularly troublesome assumption because there are data 

suggesting that the number of juvenile loggerhead sea turtles is increasing (e.g., Epperly et al. 

2007). If the increase in juvenile abundance translates into increased adult female recruitment, 

then our estimates of extinction probabilities would be overestimated; however, the relationship 

between the models with and without fishery takes would not be fundamentally changed. A 

staged matrix model, incorporating age-class survival and fecundity, would provide a much 

better evaluation tool to assess population status (and fishery impacts). 

 An example of such an evaluation is provided by the US Fish and Wildlife Service’s 

(USFWS) recent quantitative threats analysis for the Florida manatee (Trichechus manatus 

latirostris; Runge et al. 2007). The basis of this threats assessment is a comparative population 

viability analysis, which involves forecasting the Florida manatee population under different 

scenarios regarding the presence of threats, while accounting for process variation 
 

11

(environmental, demographic, and catastrophic stochasticity) and parametric and structural 

uncertainty. Several steps were required: modifying an existing population model to 

accommodate the threats analysis framework, updating survival rates, estimating the fractions of 

mortality from various causes, modeling the threats themselves, and developing metrics to 

measure the impact of the threats. While the conceptual process followed in our analysis of 

loggerhead sea turtles and that used by the USFWS are similar, the additional information 

available from the USFWS exercise results from a stage-based projection model for Florida 

manatees, incorporating environmental and demographic stochasticity, catastrophes, densitydependence, and long-term change in carrying capacity. 

 However, recent data to support such an analysis of loggerhead sea turtles are 

incomplete. A comprehensive program to collect these data should be developed and 

implemented so that scientific analyses, such as those presented here, can be improved and the 

best possible scientific advice can be provided to NOAA managers tasked with conserving both 

turtle populations and fisheries. 

ACKNOWLEDGMENTS

Thanks to Sheryan Epperly, Selina Heppell, Chris Legault, Kimberly Murray, Tim 

Ragen, Paul Richards, Fred Serchuk, Chris Sasso, and Melissa Snover for helpful comments in 

the development of this analysis and manuscript. Also, we are grateful to Blair Witherington, the 

Florida Fish and Wildlife Research Institute, and the South Carolina Department of Natural 

Resources for use of their data. Finally, Jarita Davis significantly improved the manuscript 

through her technical and grammatical edits. 
 

12

Table 1. Counts of loggerhead sea turtle (Caretta caretta) nests at index beaches for 1989-2005 

by subpopulation, biannual totals, and rates of change (λ and r) by year (NMFS in review, FWRI 

2007). 

Year Northern 

(NC, 

SC, GA) 

Peninsular 

Florida 

Total 

(Ni)

Two-year 

Running 

Sum (Rj) 

Rate of 

Change (λ) 

Inst. rate 

of change 

(r) 

1989 1,421 39,091 40,512 

1990 2,466 50,266 52,732 93,244 

1991 2,127 52,802 54,929 107,661 1.1546 0.14377 

1992 1,844 47,567 49,411 104,340 0.9692 -0.0313 

1993 931 41,808 42,739 92,150 0.8832 -0.1242 

1994 2,207 51,168 53,375 96,114 1.0430 0.04212 

1995 1,484 57843 59,327 112,702 1.1726 0.15921 

1996 1,969 52811 54,780 114,107 1.0125 0.01239 

1997 1,100 43156 44,256 99,036 0.8679 -0.1417 

1998 1,812 59918 61,730 105,986 1.0702 0.06782 

1999 2,173 56471 58,644 120,374 1.1358 0.1273 

2000 1,475 56277 57,752 116,396 0.9670 -0.0336 

2001 1,242 45941 47,183 104,935 0.9015 -0.1037 

2002 1,543 38125 39,668 86,851 0.8277 -0.1891 

2003 1,998 40726 42,724 82,392 0.9487 -0.0527 

2004 549 29547 30,096 72,820 0.8838 -0.1235 

2005 1,766 34872 36,638 66,734 0.9164 -0.0873 
 

13

Table 2. Model results based on 1989-2005 2-year running sum trend with a starting population 

size of 34,881 adult female loggerhead sea turtles (Caretta caretta) and quasi-extinction 

threshold equal to 250 adult females for base model and model with Atlantic sea scallop 

(Placopecten magellanicus) fishery takes added back into population. 

 Base 

 Model 

With Fishery 

Takes Added 

Back In 

Population Trend -0.022 -0.019 

Variance of trend 0.012 0.012 

Upper confidence limit 0.039 0.042 

Lower confidence limit -0.084 -0.080 

Quasi-extinction risk with 

95% confidence interval in 

parentheses 

@ 25 years 0.00 (0, 0) 0.00 (0, 0) 

@ 50 years 0.00 (0, 0) 0.00 (0, 0) 

@ 75 years 0.00 (0, 0.09) 0.00 (0, 0.02) 

@ 100 years 0.01 (0, 0.46) 0.01 (0, 0.31) 

Median time to extinction 207 years 240 years 
 

14

Table 3. Counts of loggerhead sea turtle (Caretta caretta) nests at index beaches for 1996-2005 

by subpopulation, biannual totals, and rates of change (λ and r) by year (NMFS in review, FWRI 

2007). Number in italics were interpolated from adjacent counts. 

Year Northern 

(NC, SC, 

GA) 

Peninsular 

Florida 

Dry 

Tortugas 

(Florida) 

Northern 

Gulf 

(FL, AL) 

Total 

(Ni)

Running 

sum 

(Rj) 

Rate of 

change 

(λ) 

Inst. rate 

of 

change 

(r) 

1996 1,969 52,811 249 166 55,195 

1997 1,100 43,156 258 166 44,680 99,875 

1998 1,812 59,918 249 149 62,128 106,808 1.0694 0.0671 

1999 2,173 56,471 292 235 59,171 121,299 1.1357 0.1272 

2000 1,475 56,277 242 181 58,175 117,346 0.9674 -0.0331 

2001 1,242 45,941 213 143 47,539 105,714 0.9009 -0.1044 

2002 1,543 38,125 210 149 40,027 87,566 0.8283 -0.1883 

2003 1,998 40,726 208 95 43,027 83,054 0.9485 -0.053 

2004 549 29,547 159 114 30,369 73,396 0.88371 -0.1236 

2005 1,766 34,872 159 120 36,917 67,286 0.91675 -0.0869 
 

15

Table 4. Model results based on 1996-2005 2-year running sum trend with a starting population 

size of 34,881 adult female loggerhead sea turtles (Caretta caretta), and quasi-extinction 

threshold equal to 250 adult females for base model and model with Atlantic sea scallop 

(Placopecten magellanicus) fishery takes added back into population. 

 Base 

 Model 

With Fishery 

Takes Added Back 

In 

Population trend -0.049 -0.046 

Variance of trend 0.011 0.011 

Upper confidence limit 0.037 0.040 

Lower confidence limit -0.135 -0.1322 

Quasi-extinction risk with 

95% confidence interval in 

parentheses 

@ 25 years 0.00 (0, 0) 0.00 (0, 0) 

@ 50 years 0.00 (0, 0.03) 0.00 (0, 0.02) 

@ 75 years 0.10 (0, 0.67) 0.06 (0, 0.57) 

@ 100 years 0.54 (0.02, 0.98) 0.42 (0.01, 0.996) 

Median time to extinction 98 years 102 years 
 

16

0

10,000

20,000

30,000

40,000

50,000

60,000

70,000

1989 1991 1993 1995 1997 1999 2001 2003 2005

Year

Count of Nests

Figure 1. Number of Atlantic Ocean loggerhead sea turtle (Caretta caretta) nests recorded at US 

Northern (NC, SC, GA) and Peninsular Florida index beaches from 1989 to 2005 (NMFS in 

review, FWRI 2007). 
 

17

0

0.1

0.2

0.3

0.4

0.5

0 20 40 60 80 100

Years in Future

Extinction Probabilities

Bootstrap Lower 95%

CI

Bootstrap Upper 95%

CI

Cumulative Extinction

Probabilities

Figure 2. Cumulative quasi-extinction probabilities and confidence intervals (CI) for 1989-2005 

base model with Atlantic sea scallop (Placopecten magellanicus) fishery takes for adult female 

western North Atlantic loggerhead sea turtles (Caretta caretta). Quasi-extinction is equal to 250 

adult female loggerhead sea turtles. 

0

0.1

0.2

0.3

0.4

0.5

0 10 20 30 40 50 60 70 80 90 100

Years in Future

Extinction Probabilities

Bootstrap Lower 95%

CI

Bootstrap Upper 95%

CI

Cumulative Extinction

Probabilites

Figure 3. Cumulative quasi-extinction probabilities and confidence intervals (CI) for 1989-2005

model with Atlantic sea scallop (Placopecten magellanicus) fishery takes for adult female 

western North Atlantic loggerhead sea turtles (Caretta caretta) added back into population. 

Quasi-extinction is equal to 250 adult female loggerhead sea turtles. 
 

18

0

0.01

0.02

0.03

0.04

0.05

0.06

0.07

0.08

0.09

0.1

0 10 20 30 40 50 60 70 80 90 10

0

Years in Future

Extinction Probabilities

With Fishery Takes -

Upper CI

With Fishery Takes

With Fishery Takes -

Lower CI

With Fishery Takes

Added Back In - Upper

CI

With Fishery Takes

Added Back In

With Fishery Takes

Added Back In - Lower

CI

Figure 4. Comparison of cumulative quasi-extinction probabilities and confidence intervals (CI) 

of 1989-2005 models with and without Atlantic sea scallop (Placopecten magellanicus) fishery 

takes. Quasi-extinction is equal to 250 adult female loggerhead sea turtles (Caretta caretta). 

Note vertical scale runs only through PEX = 0.10. 

0

0.1

0.2

0.3

0.4

0.5

0.6

0.7

0.8

0.9

1

0 10 20 30 40 50 60 70 80 90 100

Years in Future

Extinction Probabilities

1989-2005 Model With

Fishery Takes

1989-2005 Model With

Fishery Takes Added

Back In

1996-2005 Model With

Fishery Takes

1996-2005 Model With

Fishery Takes Added

Back In

Figure 5. Extinction trajectories for models with and without Atlantic sea scallop (Placopecten 

magellanicus) fishery takes with original 1989-2005 population trajectory compared to 1996-

2005 trajectory. Quasi-extinction is equal to 250 adult female loggerhead sea turtles (Caretta 

caretta). 
 

19

0

0.1

0.2

0.3

0.4

0.5

0.6

0.7

0.8

0.9

1

0 10 20 30 40 50 60 70 80 90 100

Years in Future

Extinction Probabilities

With Ten Times 

Fishery Takes

Removed

With Two Times

Fishery Takes

Removed

With Fishery Takes

Removed

With Scallop Fishery

Take

Figure 6. Cumulative quasi-extinction probabilities for 1996-2005 models with various levels of 

mortality removed from the trend. Fishery takes estimated as one time (the Atlantic sea scallop 

[Placopecten magellanicus] fisheries) versus two and ten times the original sea scallop fishery 

take level. Quasi-extinction equal to 250 adult females loggerhead sea turtles (Caretta caretta).
 

20

REFERENCES CITED

Bass AL, Epperly SP, Braun-McNeill J. 2004. Multi-year analysis of stock composition of a 

loggerhead turtle (Caretta caretta) foraging habitat using maximum likelihood and Bayesian 

methods. Cons Gen. 5:783-796. 

Bjorndal KA, Meylan AB, Turner BJ. 1983. Sea turtles nesting at Melbourne Beach, Florida. I. 

Size, growth and reproductive biology. Biol Conserv. 26:65–77 

DeMaster D, Angliss R, Cochrane J, Mace P, Merrick R, Miller M, Rumsey S, Taylor B, 

Thompson B, and R. Waples. 2004. Recommendations to NOAA Fisheries: ESA listing 

criteria by the Quantitative Working Group, 10 June 2004. NOAA Tech Memo. NMFSF/SPO-67, 85 p. 

Dennis B, Munholland PL, Scott JM.1991. Estimation of growth and extinction parameters for 

endangered species. Ecol Monogr. 61:115–143. 

Epperly S, Avens L, Garrison L, Henwood T, Hoggard W, Mitchell J, Nance J, Poffenberger J, 

Sasso C, Scott-Denton E, Yeung C. 2002. Analysis of sea turtle bycatch in the commercial 

shrimp trawl fisheries of southeast U.S waters and the Gulf of Mexico. NOAA Tech Memo. 

NMFS-SEFSC-490. 99 pp. 

Epperly S, Braun-McNeill J, Richards PM. 2007. Trends in catches rates of sea turtles in North 

Carolina, USA. Endangered Species Research 3:283-293. 

Franklin IR. 1980. Evolutionary change in small populations. In: Soule ME, Wilcox BA, editors. 

Conservation Biology: An Evolutionary-Ecological perspective. Sunderland (MA): Sinauer; 

p.135-150. 

Frazer NB, Richardson JI. 1985. Annual variation in clutch size and frequency for loggerhead 

turtles, Caretta caretta, nesting at Little Cumberland Island, Georgia, USA. Herpetologica 

41(3):246-251. 

[FWRI] Fish and Wildlife Research Institute. 2007. Sea turtle nesting feature page. 

http://research.myfwc.com/features/category_sub.asp?id=2309. Accessed March 2008. 

Ginzburg LR, Slobodkin LB, Johnson K, Bindman AG. 1982. Quasi extinction probabilities as a 

measure of impact on population growth. Risk Analysis, 21:171–181. 

Haas H, LaCasella E, Leroux R, Milliken H, Hayward B. In review. Characteristics of sea turtles 

incidentally captured in the US Atlantic sea scallop dredge fishery. Fisheries Research. 

Holmes E. 2001. Estimating risks in declining populations with poor data. PNAS. 98(9):5072-

5077. 
 

21

[IUCN] International Union for Conservation of Nature. 2008. IUCN Red List of threatened 

species: 2001 categories & criteria (version 3.1). 

http://www.iucnredlist.org/info/categories_criteria2001 

Morris W, Doak D, Groom M, Kareiva P, Fieberg J, Gerber L, Murphy P, Thompson D. 1999. 

A Practical Handbook for Population Viability Analysis. New York (NY): The Nature 

Conservancy Press; 83 pp. 

Morris WF, Doak DF. 2002. Quantitative Conservation Biology: Theory and Practice of 

Population Viability Analysis. Sunderland (MA): Sinauer; 480 pp. 

Murray KT. 2004a. Magnitude and distribution of sea turtle bycatch in the sea scallop 

(Placopecten magellanicus) dredge fishery in two areas of the Northwestern Atlantic Ocean, 

2001-2002. Fishery Bulletin. 102(4):671-681. 

Murray KT. 2004b. Bycatch of sea turtles in the Mid-Atlantic sea scallop 

(Placopecten magellanicus) dredge fishery during 2003. Northeast Fish Sci Cent Ref Doc. 

04-11; 25 pp. 

Murray KT. 2005. Total bycatch estimate of loggerhead turtles (Caretta caretta) in the 2004 

Atlantic sea scallop (Placopecten magellanicus) dredge fishery. Northeast Fish Sci Cent Ref 

Doc. 05-12; 22 pp. 

Murray KT. 2006. Estimated average annual bycatch of loggerhead sea turtles (Caretta caretta) 

in US Mid-Atlantic bottom otter trawl gear, 1996-2004. Northeast Fish Sci Cent Ref Doc. 

06-19; 26 pp. 

Murray KT. 2007. Estimated bycatch of loggerhead sea turtles (Caretta caretta) in US MidAtlantic scallop trawl gear, 2004-2005, and in sea scallop dredge gear, 2005. Northeast Fish 

Sci Cent Ref Doc 07-04; 30 pp. 

National Marine Fisheries Service (NMFS). In review. Draft recovery plan for the US Atlantic 

population of the loggerhead sea turtle (Caretta caretta). Second Revision. NOAA Tech 

Memo NMFS-FPR- ; 283 pp. 

Patterson BR, Murray DL. 2008. Flawed population viability analysis can result in misleading 

population assessment: A case study for wolves in Algonquin park, Canada. Biol Cons. 

141:669-680. 

Richardson TH, Richardson JI, Ruckdeschel C, Dix MW. 1978. Remigration patterns of 

loggerhead sea turtles (Caretta caretta) nesting on Little Cumberland Island and 

Cumberland Island, Georgia. In: Henderson G.E, editor. Proceedings of the Florida and 

interregional conference on sea turtles. St. Petersburg (FL): Florida Marine Research 

Publications Number 33; p. 39-44. 
 

22

Runge MC, Sanders-Reed CA, Langtimm CA, Fonnesbeck CJ. 2007. A quantitative threats 

analysis for the Florida manatee (Trichechus manatus latirostris). US Geological Survey 

Open-File Report 2007-1086; 34 pp. 

Schroeder BA, Foley AM, Bagley DA. 2003. Nesting patterns, reproductive migrations, and 

adult foraging areas of loggerhead turtles. In: Bolten AB, Witherington BE, editors. 

Loggerhead sea turtles. Washington (DC): Smithsonian Institute Press; p. 114–124. 

Shaffer ML. 1981. Minimum population sizes for species conservation. Biosci. 31:131-134. 

Snover M. 2005. Population trends and viability analyses for Pacific marine turtles. PIFSC 

Internal Report IR-05-008; 33 pp. 

Snover ML, Heppell S.S. In press. Application of diffusion approximation for risk assessments 

of sea turtle populations. Ecol Appl. 

[SCDNR] South Carolina Department of Natural Resources. 2006. Loggerheadlines JulyDecember 2006. http://www.dnr.sc.gov/seaturtle/lhl.htm. Accessed March 2008. 

[SEFSC] Southeast Fisheries Science Center. 2001. Stock assessments of loggerhead and 

leatherback sea turtles and an assessment of the impact of the pelagic longline fishery on the 

loggerhead and leatherback sea turtles of the western North Atlantic. NOAA Tech Memo 

NMFS-SEFSC-455; 343 pp. 

[TEWG] Turtle Expert Working Group. 1998. An assessment of the Kemp’s ridley 

(Lepidochelys kempii) and loggerhead (Caretta caretta) sea turtle populations in the western 

North Atlantic. NOAA Tech Memo NMFS-SEFSC-409; 99 pp. 

[TEWG] Turtle Expert Working Group. 2000. Assessment update for the Kemp’s ridley and 

loggerhead sea turtle populations in the western North Atlantic. NOAA Tech Memo 

NMFS-SEFSC-444; 115 pp. 

Wallace BP, Heppell SS, Lewison RL, Kelez S, Crowder LB. In press. Reproductive values of 

loggerhead turtles in fisheries bycatch worldwide. J Appl Ecol. 

Witherington B, Herren R, Bresette M. 2006. Caretta caretta – loggerhead sea turtle. 

Chelonian Res Mono. 3:74-89. 

Witherington B, Kubilis P, Brost B, Meylan A. In review. Decreasing annual nest counts in a 

globally important loggerhead sea turtle population. Ecol Appl.