Many studies of pond-breeding amphibians involve sampling individuals during migration to and from breeding habitats. Interpreting population processes and dynamics from these studies is difficult because (1) only a proportion of the population is observable each season, while an unknown proportion remains unobservable (e.g., non-breeding adults) and (2) not all observable animals are captured. Imperfect capture probability can be easily accommodated in capture-recapture models, but temporary transitions between observable and unobservable states, often referred to as temporary emigration, is known to cause problems in both open- and closed-population models. We develop a multistate mark-recapture (MSMR) model, using an open-robust design that permits one entry and one exit from the study area per season. Our method extends previous temporary emigration models (MSMR with an unobservable state) in two ways. First, we relax the assumption of demographic closure (no mortality) between consecutive (secondary) samples, allowing estimation of within-pond survival. Also, we add the flexibility to express survival probability of unobservable individuals (e.g., ‘‘non-breeders’’) as a function of the survival probability of observable animals while in the same, terrestrial habitat. This allows for potentially different annual survival probabilities for observable and unobservable animals. We apply our model to a relictual population of eastern tiger salamanders (Ambystoma tigrinum tigrinum). Despite small sample sizes, demographic parameters were estimated with reasonable precision. We tested several a priori biological hypotheses and found evidence for seasonal differences in pond survival. Our methods could be applied to a variety of pond-breeding species and other taxa where individuals are captured entering or exiting a common area (e.g., spawning or roosting area, hibernacula).
","language":"English","publisher":"Wiley","doi":"10.1890/03-0539","usgsCitation":"Bailey, L., Kendall, W., Church, D., and Wilbur, H., 2004, Estimating survival and breeding probability for pond-breeding amphibians: a modified robust design: Ecology, v. 85, no. 9, p. 2456-2466, https://doi.org/10.1890/03-0539.","productDescription":"11 p.","startPage":"2456","endPage":"2466","costCenters":[{"id":531,"text":"Patuxent Wildlife Research Center","active":true,"usgs":true}],"links":[{"id":498889,"rank":1,"type":{"id":40,"text":"Open Access Publisher Index Page"},"url":"https://doi.org/10.1890/03-0539","text":"Publisher Index Page"},{"id":202291,"rank":0,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"}],"volume":"85","issue":"9","noUsgsAuthors":false,"publicationStatus":"PW","scienceBaseUri":"4f4e4a0ce4b07f02db5fc81c","contributors":{"authors":[{"text":"Bailey, L.L. 0000-0002-5959-2018","orcid":"https://orcid.org/0000-0002-5959-2018","contributorId":61006,"corporation":false,"usgs":true,"family":"Bailey","given":"L.L.","affiliations":[],"preferred":false,"id":341306,"contributorType":{"id":1,"text":"Authors"},"rank":1},{"text":"Kendall, W. L. 0000-0003-0084-9891","orcid":"https://orcid.org/0000-0003-0084-9891","contributorId":32880,"corporation":false,"usgs":true,"family":"Kendall","given":"W. L.","affiliations":[{"id":531,"text":"Patuxent Wildlife Research Center","active":true,"usgs":true}],"preferred":false,"id":341303,"contributorType":{"id":1,"text":"Authors"},"rank":2},{"text":"Church, D.R.","contributorId":51884,"corporation":false,"usgs":true,"family":"Church","given":"D.R.","email":"","affiliations":[],"preferred":false,"id":341304,"contributorType":{"id":1,"text":"Authors"},"rank":3},{"text":"Wilbur, H.M.","contributorId":54326,"corporation":false,"usgs":true,"family":"Wilbur","given":"H.M.","email":"","affiliations":[],"preferred":false,"id":341305,"contributorType":{"id":1,"text":"Authors"},"rank":4}]}} ,{"id":5224332,"text":"5224332 - 2004 - Levels of fecal corticosterone in sandhill cranes during a human-led migration","interactions":[],"lastModifiedDate":"2021-09-28T17:25:08.306741","indexId":"5224332","displayToPublicDate":"2010-06-16T12:18:53","publicationYear":"2004","noYear":false,"publicationType":{"id":2,"text":"Article"},"publicationSubtype":{"id":10,"text":"Journal Article"},"seriesTitle":{"id":2507,"text":"Journal of Wildlife Diseases","active":true,"publicationSubtype":{"id":10}},"title":"Levels of fecal corticosterone in sandhill cranes during a human-led migration","docAbstract":"Fourteen captive-reared greater sandhill cranes (Grus canadensis tabida) were conditioned to follow ultralight aircraft to promote migration between Wisconsin and Florida (USA) after release. Fecal samples were collected throughout the training period in Wisconsin and during a 1,977-km human-led migration to Florida to determine fecal corticosterone (FC) concentrations by radioimmunoassay. The mean (±SE) FC concentration during the training period was 109.5±7.5 ng/g and was representative of baseline levels recorded previously from sandhill cranes. Fecal corticosterone concentrations increased in early migration compared to concentrations 1 mo prior to departure (P<0.01) but were not different from baseline concentrations at the end of the 6-wk migration period. The variability of FC concentrations in individual samples was greater throughout the migration than the training period. Increases in FC during migration were modest and generally consistent with normal corticosterone elevations observed in migrating birds.
","language":"English","publisher":"Wildlife Disease Association","doi":"10.7589/0090-3558-40.2.267","usgsCitation":"Hartup, B., Olsen, G.H., Czekala, N.M., Paul-Murphy, J., and Langenberg, J., 2004, Levels of fecal corticosterone in sandhill cranes during a human-led migration: Journal of Wildlife Diseases, v. 40, no. 2, p. 267-272, https://doi.org/10.7589/0090-3558-40.2.267.","productDescription":"6 p.","startPage":"267","endPage":"272","costCenters":[{"id":531,"text":"Patuxent Wildlife Research Center","active":true,"usgs":true}],"links":[{"id":477987,"rank":1,"type":{"id":41,"text":"Open Access External Repository Page"},"url":"http://www.bioone.org/doi/10.7589/0090-3558-40.2.267","text":"External Repository"},{"id":197742,"rank":0,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"}],"country":"United States","state":"Florida, Wisconsin","volume":"40","issue":"2","noUsgsAuthors":false,"publicationStatus":"PW","scienceBaseUri":"4f4e4b16e4b07f02db6a5570","contributors":{"authors":[{"text":"Hartup, B.K.","contributorId":16367,"corporation":false,"usgs":true,"family":"Hartup","given":"B.K.","email":"","affiliations":[],"preferred":false,"id":341307,"contributorType":{"id":1,"text":"Authors"},"rank":1},{"text":"Olsen, Glenn H. 0000-0002-7188-6203 golsen@usgs.gov","orcid":"https://orcid.org/0000-0002-7188-6203","contributorId":40918,"corporation":false,"usgs":true,"family":"Olsen","given":"Glenn","email":"golsen@usgs.gov","middleInitial":"H.","affiliations":[{"id":531,"text":"Patuxent Wildlife Research Center","active":true,"usgs":true}],"preferred":false,"id":341308,"contributorType":{"id":1,"text":"Authors"},"rank":2},{"text":"Czekala, Nancy M.","contributorId":81214,"corporation":false,"usgs":true,"family":"Czekala","given":"Nancy","email":"","middleInitial":"M.","affiliations":[],"preferred":false,"id":341310,"contributorType":{"id":1,"text":"Authors"},"rank":3},{"text":"Paul-Murphy, J.","contributorId":55110,"corporation":false,"usgs":true,"family":"Paul-Murphy","given":"J.","affiliations":[],"preferred":false,"id":341309,"contributorType":{"id":1,"text":"Authors"},"rank":4},{"text":"Langenberg, J.A.","contributorId":91055,"corporation":false,"usgs":true,"family":"Langenberg","given":"J.A.","email":"","affiliations":[],"preferred":false,"id":341311,"contributorType":{"id":1,"text":"Authors"},"rank":5}]}} ,{"id":5224322,"text":"5224322 - 2004 - Capture-recapture analysis for estimating manatee reproductive rates","interactions":[],"lastModifiedDate":"2015-12-16T08:26:14","indexId":"5224322","displayToPublicDate":"2010-06-16T12:18:52","publicationYear":"2004","noYear":false,"publicationType":{"id":2,"text":"Article"},"publicationSubtype":{"id":10,"text":"Journal Article"},"seriesTitle":{"id":2671,"text":"Marine Mammal Science","active":true,"publicationSubtype":{"id":10}},"title":"Capture-recapture analysis for estimating manatee reproductive rates","docAbstract":"Modeling the life history of the endangered Florida manatee (Trichechus manatus latirostris) is an important step toward understanding its population dynamics and predicting its response to management actions. We developed a multi-state mark-resighting model for data collected under Pollock's robust design. This model estimates breeding probability conditional on a female's breeding state in the previous year; assumes sighting probability depends on breeding state; and corrects for misclassification of a cow with first-year calf, by estimating conditional sighting probability for the calf. The model is also appropriate for estimating survival and unconditional breeding probabilities when the study area is closed to temporary emigration across years. We applied this model to photo-identification data for the Northwest and Atlantic Coast populations of manatees, for years 1982?2000. With rare exceptions, manatees do not reproduce in two consecutive years. For those without a first-year calf in the previous year, the best-fitting model included constant probabilities of producing a calf for the Northwest (0.43, SE = 0.057) and Atlantic (0.38, SE = 0.045) populations. The approach we present to adjust for misclassification of breeding state could be applicable to a large number of marine mammal populations.
","language":"English","publisher":"Wiley","doi":"10.1111/j.1748-7692.2004.tb01170.x","usgsCitation":"Kendall, W., Langtimm, C., Beck, C., and Runge, M., 2004, Capture-recapture analysis for estimating manatee reproductive rates: Marine Mammal Science, v. 20, no. 3, p. 424-437, https://doi.org/10.1111/j.1748-7692.2004.tb01170.x.","productDescription":"14 p.","startPage":"424","endPage":"437","onlineOnly":"N","additionalOnlineFiles":"N","costCenters":[{"id":531,"text":"Patuxent Wildlife Research Center","active":true,"usgs":true}],"links":[{"id":198244,"rank":1,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"}],"volume":"20","issue":"3","noUsgsAuthors":false,"publicationDate":"2006-08-26","publicationStatus":"PW","scienceBaseUri":"4f4e49fde4b07f02db5f5fab","contributors":{"authors":[{"text":"Kendall, W. L. 0000-0003-0084-9891","orcid":"https://orcid.org/0000-0003-0084-9891","contributorId":32880,"corporation":false,"usgs":true,"family":"Kendall","given":"W. L.","affiliations":[{"id":531,"text":"Patuxent Wildlife Research Center","active":true,"usgs":true}],"preferred":false,"id":341272,"contributorType":{"id":1,"text":"Authors"},"rank":1},{"text":"Langtimm, C.A. 0000-0001-8499-5743","orcid":"https://orcid.org/0000-0001-8499-5743","contributorId":71133,"corporation":false,"usgs":false,"family":"Langtimm","given":"C.A.","affiliations":[],"preferred":false,"id":341274,"contributorType":{"id":1,"text":"Authors"},"rank":2},{"text":"Beck, C.A. 0000-0002-5388-5418","orcid":"https://orcid.org/0000-0002-5388-5418","contributorId":78674,"corporation":false,"usgs":true,"family":"Beck","given":"C.A.","affiliations":[],"preferred":false,"id":341275,"contributorType":{"id":1,"text":"Authors"},"rank":3},{"text":"Runge, M.C. 0000-0002-8081-536X","orcid":"https://orcid.org/0000-0002-8081-536X","contributorId":49312,"corporation":false,"usgs":true,"family":"Runge","given":"M.C.","affiliations":[],"preferred":false,"id":341273,"contributorType":{"id":1,"text":"Authors"},"rank":4}]}} ,{"id":5224317,"text":"5224317 - 2004 - Sex ratio estimation and survival analysis for Orthetrum coerulescens (Odonata, Libellulidae)","interactions":[],"lastModifiedDate":"2021-07-21T16:59:07.527578","indexId":"5224317","displayToPublicDate":"2010-06-16T12:18:52","publicationYear":"2004","noYear":false,"publicationType":{"id":2,"text":"Article"},"publicationSubtype":{"id":10,"text":"Journal Article"},"seriesTitle":{"id":1176,"text":"Canadian Journal of Zoology","active":true,"publicationSubtype":{"id":10}},"displayTitle":"Sex ratio estimation and survival analysis for Orthetrum coerulescens (Odonata, Libellulidae)","title":"Sex ratio estimation and survival analysis for Orthetrum coerulescens (Odonata, Libellulidae)","docAbstract":"There is controversy over whether uneven sex ratios observed in mature dragonfly populations are a mere artifact resulting from the higher observability of males. Previous studies have at best made indirect inference about sex ratios by analysis of survival or recapture rates. Here, we obtain direct estimates of sex ratio from capture-recapture data based on the Cormack-Jolly-Seber model. We studied Orthetrum coerulescens (Fabricius, 1798) at three sites in the Swiss Jura Mountains over an entire activity period. Recapture rates per 5-day interval were 3.5 times greater for males (0.67, SE 0.02) than for females (0.19, SE 0.02). At two sites, recapture rate increased over the season for males and was constant for females, and at one site it decreased with precipitation for both sexes. In addition, recapture rate was higher with higher temperature for males only. We found no evidence for higher male survival rates in any population. Survival per 5-day interval for both sexes was estimated to be 0.77 (95% CI 0.75–0.79) without significant site or time-specific variation. There were clear effects of temperature (positive) and precipitation (negative) on survival rate at two sites. Direct estimates of sex ratios were not significantly different from 1 for any time interval. Hence, the observed male-biased sex ratio in adult O. coerulescens was an artifact resulting from the better observability of males. The method presented in this paper is applicable to sex ratio estimation in any kind of animal.
","language":"English","publisher":"Canadian Science Publishing","doi":"10.1139/z04-004","usgsCitation":"Kery, M., and Juillerat, L., 2004, Sex ratio estimation and survival analysis for Orthetrum coerulescens (Odonata, Libellulidae): Canadian Journal of Zoology, v. 82, no. 3, p. 399-406, https://doi.org/10.1139/z04-004.","productDescription":"8","startPage":"399","endPage":"406","costCenters":[{"id":531,"text":"Patuxent Wildlife Research Center","active":true,"usgs":true}],"links":[{"id":201739,"rank":0,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"}],"country":"Switzerland","otherGeospatial":"Jura Mountains","geographicExtents":"{\n \"type\": \"FeatureCollection\",\n \"features\": [\n {\n \"type\": \"Feature\",\n \"properties\": {},\n \"geometry\": {\n \"type\": \"Polygon\",\n \"coordinates\": [\n [\n [\n 6.921386718750007,\n 47.502358951968574\n ],\n [\n 6.547851562500008,\n 47.100044694025215\n ],\n [\n 5.932617187500008,\n 46.32417161725691\n ],\n [\n 5.888671875000007,\n 46.14939437647686\n ],\n [\n 6.108398437500008,\n 46.08085173686784\n ],\n [\n 6.679687500000008,\n 46.33175800051563\n ],\n [\n 6.844482421875007,\n 46.057985244793024\n ],\n [\n 7.261962890625007,\n 45.82114340079471\n ],\n [\n 7.965087890625,\n 45.92822950933618\n ],\n [\n 8.426513671875,\n 46.17983040759436\n ],\n [\n 8.931884765625,\n 45.882360730184025\n ],\n [\n 9.437255859375,\n 46.21785176740299\n ],\n [\n 10.030517578125,\n 46.18743678432541\n ],\n [\n 10.6787109375,\n 46.53619267489863\n ],\n [\n 10.48095703125,\n 46.98025235521883\n ],\n [\n 9.876708984375,\n 47.12995075666307\n ],\n [\n 9.6240234375,\n 47.52461999690651\n ],\n [\n 8.81103515625,\n 47.73193447949174\n ],\n [\n 7.415771484375003,\n 47.65058757118736\n ],\n [\n 6.921386718750007,\n 47.502358951968574\n ]\n ]\n ]\n }\n }\n ]\n}","volume":"82","issue":"3","noUsgsAuthors":false,"publicationStatus":"PW","scienceBaseUri":"4f4e49fbe4b07f02db5f4b2e","contributors":{"authors":[{"text":"Kery, M.","contributorId":46637,"corporation":false,"usgs":true,"family":"Kery","given":"M.","affiliations":[],"preferred":false,"id":341254,"contributorType":{"id":1,"text":"Authors"},"rank":1},{"text":"Juillerat, L.","contributorId":45426,"corporation":false,"usgs":true,"family":"Juillerat","given":"L.","email":"","affiliations":[],"preferred":false,"id":341253,"contributorType":{"id":1,"text":"Authors"},"rank":2}]}} ,{"id":5224328,"text":"5224328 - 2004 - The importance of environmental variability and management control error to optimal harvest policies","interactions":[],"lastModifiedDate":"2021-10-04T17:59:50.866036","indexId":"5224328","displayToPublicDate":"2010-06-16T12:18:52","publicationYear":"2004","noYear":false,"publicationType":{"id":2,"text":"Article"},"publicationSubtype":{"id":10,"text":"Journal Article"},"seriesTitle":{"id":2508,"text":"Journal of Wildlife Management","active":true,"publicationSubtype":{"id":10}},"title":"The importance of environmental variability and management control error to optimal harvest policies","docAbstract":"State-dependent strategies (SDSs) are the most general form of harvest policy because they allow the harvest rate to depend, without constraint, on the state of the system. State-dependent strategies that provide an optimal harvest rate for any system state can be calculated, and stochasticity can be appropriately accommodated in this optimization. Stochasticity poses 2 challenges to harvest policies: (1) the population will never be at the equilibrium state; and (2) stochasticity induces uncertainty about future states. We investigated the effects of 2 types of stochasticity, environmental variability and management control error, on SDS harvest policies for a white-tailed deer (Odocoileus virginianus) model, and contrasted these with a harvest policy based on maximum sustainable yield (MSY). Increasing stochasticity resulted in more conservative SDSs; that is, higher population densities were required to support the same harvest rate, but these effects were generally small. As stochastic effects increased, SDSs performed much better than MSY. Both deterministic and stochastic SDSs maintained maximum mean annual harvest yield (AHY) and optimal equilibrium population size (Neq) in a stochastic environment, whereas an MSY policy could not. We suggest 3 rules of thumb for harvest management of long-lived vertebrates in stochastic systems: (1) an SDS is advantageous over an MSY policy, (2) using an SDS rather than an MSY is more important than whether a deterministic or stochastic SDS is used, and (3) for SDSs, rankings of the variability in management outcomes (e.g., harvest yield) resulting from parameter stochasticity can be predicted by rankings of the deterministic elasticities.
","language":"English","publisher":"BioOne Complete","doi":"10.2193/0022-541X(2004)068[0585:TIOEVA]2.0.CO;2","usgsCitation":"Hunter, C., and Runge, M., 2004, The importance of environmental variability and management control error to optimal harvest policies: Journal of Wildlife Management, v. 68, no. 3, p. 585-594, https://doi.org/10.2193/0022-541X(2004)068[0585:TIOEVA]2.0.CO;2.","productDescription":"10 p.","startPage":"585","endPage":"594","costCenters":[{"id":531,"text":"Patuxent Wildlife Research Center","active":true,"usgs":true}],"links":[{"id":201657,"rank":0,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"}],"volume":"68","issue":"3","noUsgsAuthors":false,"publicationStatus":"PW","scienceBaseUri":"4f4e4a85e4b07f02db64d618","contributors":{"authors":[{"text":"Hunter, C.M.","contributorId":19670,"corporation":false,"usgs":true,"family":"Hunter","given":"C.M.","email":"","affiliations":[],"preferred":false,"id":341294,"contributorType":{"id":1,"text":"Authors"},"rank":1},{"text":"Runge, M.C. 0000-0002-8081-536X","orcid":"https://orcid.org/0000-0002-8081-536X","contributorId":49312,"corporation":false,"usgs":true,"family":"Runge","given":"M.C.","affiliations":[],"preferred":false,"id":341295,"contributorType":{"id":1,"text":"Authors"},"rank":2}]}} ,{"id":5224325,"text":"5224325 - 2004 - Estimation of tiger densities in the tropical dry forests of Panna, Central India, using photographic capture-recapture sampling","interactions":[],"lastModifiedDate":"2016-10-27T12:12:48","indexId":"5224325","displayToPublicDate":"2010-06-16T12:18:52","publicationYear":"2004","noYear":false,"publicationType":{"id":2,"text":"Article"},"publicationSubtype":{"id":10,"text":"Journal Article"},"seriesTitle":{"id":774,"text":"Animal Conservation","active":true,"publicationSubtype":{"id":10}},"title":"Estimation of tiger densities in the tropical dry forests of Panna, Central India, using photographic capture-recapture sampling","docAbstract":"Tropical dry-deciduous forests comprise more than 45% of the tiger (Panthera tigris) habitat in India. However, in the absence of rigorously derived estimates of ecological densities of tigers in dry forests, critical baseline data for managing tiger populations are lacking. In this study tiger densities were estimated using photographic capture–recapture sampling in the dry forests of Panna Tiger Reserve in Central India. Over a 45-day survey period, 60 camera trap sites were sampled in a well-protected part of the 542-km2 reserve during 2002. A total sampling effort of 914 camera-trap-days yielded photo-captures of 11 individual tigers over 15 sampling occasions that effectively covered a 418-km2 area. The closed capture–recapture model Mh, which incorporates individual heterogeneity in capture probabilities, fitted these photographic capture history data well. The estimated capture probability/sample, p̂= 0.04, resulted in an estimated tiger population size and standard error (N̂(SÊN̂)) of 29 (9.65), and a density (D̂(SÊD̂)) of 6.94 (3.23) tigers/100 km2. The estimated tiger density matched predictions based on prey abundance. Our results suggest that, if managed appropriately, the available dry forest habitat in India has the potential to support a population size of about 9000 wild tigers.
","language":"English","publisher":"Wiley","doi":"10.1017/S1367943004001477","usgsCitation":"Karanth, K., Chundawat, R.S., Nichols, J., and Kumar, N.S., 2004, Estimation of tiger densities in the tropical dry forests of Panna, Central India, using photographic capture-recapture sampling: Animal Conservation, v. 7, no. 3, p. 285-290, https://doi.org/10.1017/S1367943004001477.","productDescription":"6 p.","startPage":"285","endPage":"290","numberOfPages":"6","costCenters":[{"id":531,"text":"Patuxent Wildlife Research Center","active":true,"usgs":true}],"links":[{"id":203050,"rank":0,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"}],"volume":"7","issue":"3","noUsgsAuthors":false,"publicationDate":"2006-02-28","publicationStatus":"PW","scienceBaseUri":"4f4e4a0ae4b07f02db5fb20b","contributors":{"authors":[{"text":"Karanth, K.Ullas","contributorId":112954,"corporation":false,"usgs":true,"family":"Karanth","given":"K.Ullas","email":"","affiliations":[],"preferred":false,"id":341290,"contributorType":{"id":1,"text":"Authors"},"rank":1},{"text":"Chundawat, Raghunandan S.","contributorId":81607,"corporation":false,"usgs":true,"family":"Chundawat","given":"Raghunandan","email":"","middleInitial":"S.","affiliations":[],"preferred":false,"id":341291,"contributorType":{"id":1,"text":"Authors"},"rank":2},{"text":"Nichols, James D. jnichols@usgs.gov","contributorId":139082,"corporation":false,"usgs":true,"family":"Nichols","given":"James D.","email":"jnichols@usgs.gov","affiliations":[{"id":531,"text":"Patuxent Wildlife Research Center","active":true,"usgs":true}],"preferred":false,"id":341288,"contributorType":{"id":1,"text":"Authors"},"rank":3},{"text":"Kumar, N. Samba","contributorId":52701,"corporation":false,"usgs":true,"family":"Kumar","given":"N.","email":"","middleInitial":"Samba","affiliations":[],"preferred":false,"id":341289,"contributorType":{"id":1,"text":"Authors"},"rank":4}]}} ,{"id":5224321,"text":"5224321 - 2004 - A stage-based model of manatee population dynamics","interactions":[],"lastModifiedDate":"2015-12-16T09:02:47","indexId":"5224321","displayToPublicDate":"2010-06-16T12:18:52","publicationYear":"2004","noYear":false,"publicationType":{"id":2,"text":"Article"},"publicationSubtype":{"id":10,"text":"Journal Article"},"seriesTitle":{"id":2671,"text":"Marine Mammal Science","active":true,"publicationSubtype":{"id":10}},"title":"A stage-based model of manatee population dynamics","docAbstract":"A stage-structured population model for the Florida manatee (Trichechus manatus latirostris) was developed that explicitly incorporates uncertainty in parameter estimates. The growth rates calculated with this model reflect the status of the regional populations over the most recent 10-yr period. The Northwest and Upper St. Johns River regions have growth rates (8) of 1.037 (95% interval, 1.016?1.056) and 1.062 (1.037?1.081), respectively. The Southwest region has a growth rate of 0.989 (0.946?1.024), suggesting this population has been declining at about 1.1% per year. The estimated growth rate in the Atlantic region is 1.010 (0.988?1.029), but there is some uncertainty about whether adult survival rates have been constant over the last 10 yr; using the mean survival rates from the most recent 5-yr period, the estimated growth rate in this region is 0.970 (0.938?0.998). Elasticity analysis indicates that the most effective management actions should seek to increase adult survival rates. Decomposition of the uncertainty in the growth rates indicates that uncertainty about population status can best be reduced through increased monitoring of adult survival rate.
","language":"English","publisher":"Wiley","doi":"10.1111/j.1748-7692.2004.tb01167.x","usgsCitation":"Runge, M., Langtimm, C., and Kendall, W., 2004, A stage-based model of manatee population dynamics: Marine Mammal Science, v. 20, no. 3, p. 361-385, https://doi.org/10.1111/j.1748-7692.2004.tb01167.x.","productDescription":"25 p.","startPage":"361","endPage":"385","onlineOnly":"N","additionalOnlineFiles":"N","costCenters":[{"id":531,"text":"Patuxent Wildlife Research Center","active":true,"usgs":true}],"links":[{"id":477988,"rank":2,"type":{"id":40,"text":"Open Access Publisher Index Page"},"url":"https://doi.org/10.1111/j.1748-7692.2004.tb01167.x","text":"Publisher Index Page"},{"id":202322,"rank":1,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"}],"volume":"20","issue":"3","noUsgsAuthors":false,"publicationDate":"2006-08-26","publicationStatus":"PW","scienceBaseUri":"4f4e4b17e4b07f02db6a6319","contributors":{"authors":[{"text":"Runge, M.C. 0000-0002-8081-536X","orcid":"https://orcid.org/0000-0002-8081-536X","contributorId":49312,"corporation":false,"usgs":true,"family":"Runge","given":"M.C.","affiliations":[],"preferred":false,"id":341270,"contributorType":{"id":1,"text":"Authors"},"rank":1},{"text":"Langtimm, C.A. 0000-0001-8499-5743","orcid":"https://orcid.org/0000-0001-8499-5743","contributorId":71133,"corporation":false,"usgs":false,"family":"Langtimm","given":"C.A.","affiliations":[],"preferred":false,"id":341271,"contributorType":{"id":1,"text":"Authors"},"rank":2},{"text":"Kendall, W. L. 0000-0003-0084-9891","orcid":"https://orcid.org/0000-0003-0084-9891","contributorId":32880,"corporation":false,"usgs":true,"family":"Kendall","given":"W. L.","affiliations":[{"id":531,"text":"Patuxent Wildlife Research Center","active":true,"usgs":true}],"preferred":false,"id":341269,"contributorType":{"id":1,"text":"Authors"},"rank":3}]}} ,{"id":5224303,"text":"5224303 - 2004 - Investigating species co-occurrence patterns when species are detected imperfectly","interactions":[],"lastModifiedDate":"2021-08-30T15:42:59.828089","indexId":"5224303","displayToPublicDate":"2010-06-16T12:18:50","publicationYear":"2004","noYear":false,"publicationType":{"id":2,"text":"Article"},"publicationSubtype":{"id":10,"text":"Journal Article"},"seriesTitle":{"id":2158,"text":"Journal of Animal Ecology","active":true,"publicationSubtype":{"id":10}},"title":"Investigating species co-occurrence patterns when species are detected imperfectly","docAbstract":"1. Over the last 30 years there has been a great deal of interest in investigating patterns of species co-occurrence across a number of locations, which has led to the development of numerous methods to determine whether there is evidence that a particular pattern may not have occurred by random chance. 2. A key aspect that seems to have been largely overlooked is the possibility that species may not always be detected at a location when present, which leads to 'false absences' in a species presence/absence matrix that may cause incorrect inferences to be made about co-occurrence patterns. Furthermore, many of the published methods for investigating patterns of species co-occurrence do not account for potential differences in the site characteristics that may partially (at least) explain non-random patterns (e.g. due to species having similar/different habitat preferences). 3. Here we present a statistical method for modelling co-occurrence patterns between species while accounting for imperfect detection and site characteristics. This method requires that multiple presence/absence surveys for the species be conducted over a reasonably short period of time at most sites. The method yields unbiased estimates of probabilities of occurrence, and is practical when the number of species is small (< 4). 4. To illustrate the method we consider data collected on two terrestrial salamander species, Plethodon jordani and members of the Plethodon glutinosus complex, collected in the Great Smoky Mountains National Park, USA. We find no evidence that the species do not occur independently at sites once site elevation has been allowed for, although we find some evidence of a statistical interaction between species in terms of detectability that we suggest may be due to changes in relative abundances.
","language":"English","publisher":"Wiley","doi":"10.1111/j.0021-8790.2004.00828.x","usgsCitation":"MacKenzie, D., Bailey, L., and Nichols, J., 2004, Investigating species co-occurrence patterns when species are detected imperfectly: Journal of Animal Ecology, v. 73, no. 3, p. 546-555, https://doi.org/10.1111/j.0021-8790.2004.00828.x.","productDescription":"10 p.","startPage":"546","endPage":"555","costCenters":[{"id":531,"text":"Patuxent Wildlife Research Center","active":true,"usgs":true}],"links":[{"id":477994,"rank":1,"type":{"id":40,"text":"Open Access Publisher Index Page"},"url":"https://doi.org/10.1111/j.0021-8790.2004.00828.x","text":"Publisher Index Page"},{"id":199464,"rank":0,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"}],"country":"United States","state":"North Carolina, Tennessee","otherGeospatial":"Great Smoky Mountains National Park","geographicExtents":"{\n \"type\": \"FeatureCollection\",\n \"features\": [\n {\n \"type\": \"Feature\",\n \"properties\": {},\n \"geometry\": {\n \"type\": \"Polygon\",\n \"coordinates\": [\n [\n [\n -83.968505859375,\n 35.29943548054545\n ],\n [\n -83.0126953125,\n 35.29943548054545\n ],\n [\n -83.0126953125,\n 35.746512259918504\n ],\n [\n -83.968505859375,\n 35.746512259918504\n ],\n [\n -83.968505859375,\n 35.29943548054545\n ]\n ]\n ]\n }\n }\n ]\n}","volume":"73","issue":"3","noUsgsAuthors":false,"publicationDate":"2004-04-16","publicationStatus":"PW","scienceBaseUri":"4f4e4b05e4b07f02db699fe6","contributors":{"authors":[{"text":"MacKenzie, D.I.","contributorId":69522,"corporation":false,"usgs":true,"family":"MacKenzie","given":"D.I.","email":"","affiliations":[],"preferred":false,"id":341203,"contributorType":{"id":1,"text":"Authors"},"rank":1},{"text":"Bailey, L.L. 0000-0002-5959-2018","orcid":"https://orcid.org/0000-0002-5959-2018","contributorId":61006,"corporation":false,"usgs":true,"family":"Bailey","given":"L.L.","affiliations":[],"preferred":false,"id":341202,"contributorType":{"id":1,"text":"Authors"},"rank":2},{"text":"Nichols, J.D. 0000-0002-7631-2890","orcid":"https://orcid.org/0000-0002-7631-2890","contributorId":14332,"corporation":false,"usgs":true,"family":"Nichols","given":"J.D.","affiliations":[],"preferred":false,"id":341201,"contributorType":{"id":1,"text":"Authors"},"rank":3}]}} ,{"id":5224310,"text":"5224310 - 2004 - Native bees and plant pollination","interactions":[],"lastModifiedDate":"2012-02-02T00:15:04","indexId":"5224310","displayToPublicDate":"2010-06-16T12:18:50","publicationYear":"2004","noYear":false,"publicationType":{"id":2,"text":"Article"},"publicationSubtype":{"id":10,"text":"Journal Article"},"seriesTitle":{"id":3296,"text":"Rhode Island Naturalist","active":true,"publicationSubtype":{"id":10}},"title":"Native bees and plant pollination","docAbstract":"Bees are important pollinators, but evidence suggests that numbers of some species are declining. Decreases have been documented in the honey bee, Apis mellifera (which was introduced to North America), but there are no monitoring programs for the vast majority of native species, so we cannot be sure about the extent of this problem. Recent efforts to develop standardized protocols for bee sampling will help us collect the data needed to assess trends in bee populations. Unfortunately, diversity of bee life cycles and phenologies, and the large number of rare species, make it difficult to assess trends in bee faunas. Changes in bee populations can affect plant reproduction, which can influence plant population density and cover, thus potentially modifying horizontal and vertical structure of a community, microclimate near the ground, patterns of nitrogen deposition, etc. These potential effects of changes in pollination patterns have not been assessed in natural communities. Effects of management actions on bees and other pollinators should be considered in conservation planning. ","largerWorkType":{"id":2,"text":"Article"},"largerWorkTitle":"Rhode Island Naturalist","largerWorkSubtype":{"id":10,"text":"Journal Article"},"language":"English","collaboration":"6159_Ginsberg.pdf","usgsCitation":"Ginsberg, H., 2004, Native bees and plant pollination: Rhode Island Naturalist, v. 11, no. 1, p. 1-3.","productDescription":"1-3","startPage":"1","endPage":"3","numberOfPages":"3","costCenters":[{"id":531,"text":"Patuxent Wildlife Research Center","active":true,"usgs":true}],"links":[{"id":198141,"rank":0,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"}],"volume":"11","issue":"1","noUsgsAuthors":false,"publicationStatus":"PW","scienceBaseUri":"4f4e4b28e4b07f02db6b10dc","contributors":{"authors":[{"text":"Ginsberg, H. S. 0000-0002-4933-2466","orcid":"https://orcid.org/0000-0002-4933-2466","contributorId":27576,"corporation":false,"usgs":true,"family":"Ginsberg","given":"H. S.","affiliations":[],"preferred":false,"id":341232,"contributorType":{"id":1,"text":"Authors"},"rank":1}]}} ,{"id":5224302,"text":"5224302 - 2004 - Tigers and their prey: Predicting carnivore densities from prey abundance","interactions":[],"lastModifiedDate":"2021-10-18T17:26:08.209649","indexId":"5224302","displayToPublicDate":"2010-06-16T12:18:50","publicationYear":"2004","noYear":false,"publicationType":{"id":2,"text":"Article"},"publicationSubtype":{"id":10,"text":"Journal Article"},"seriesTitle":{"id":3164,"text":"Proceedings of the National Academy of Sciences","active":true,"publicationSubtype":{"id":10}},"title":"Tigers and their prey: Predicting carnivore densities from prey abundance","docAbstract":"The goal of ecology is to understand interactions that determine the distribution and abundance of organisms. In principle, ecologists should be able to identify a small number of limiting resources for a species of interest, estimate densities of these resources at different locations across the landscape, and then use these estimates to predict the density of the focal species at these locations. In practice, however, development of functional relationships between abundances of species and their resources has proven extremely difficult, and examples of such predictive ability are very rare. Ecological studies of prey requirements of tigers Panthera tigris led us to develop a simple mechanistic model for predicting tiger density as a function of prey density. We tested our model using data from a landscape-scale long-term (1995-2003) field study that estimated tiger and prey densities in 11 ecologically diverse sites across India. We used field techniques and analytical methods that specifically addressed sampling and detectability, two issues that frequently present problems in macroecological studies of animal populations. Estimated densities of ungulate prey ranged between 5.3 and 63.8 animals per km2. Estimated tiger densities (3.2-16.8 tigers per 100 km2) were reasonably consistent with model predictions. The results provide evidence of a functional relationship between abundances of large carnivores and their prey under a wide range of ecological conditions. In addition to generating important insights into carnivore ecology and conservation, the study provides a potentially useful model for the rigorous conduct of macroecological science.
","language":"English","publisher":"Proceedings of the National Academy of Sciences","doi":"10.1073/pnas.0306210101","usgsCitation":"Karanth, K.U., Nichols, J., Kumar, S., Link, W., and Hines, J., 2004, Tigers and their prey: Predicting carnivore densities from prey abundance: Proceedings of the National Academy of Sciences, v. 101, no. 14, p. 4854-4858, https://doi.org/10.1073/pnas.0306210101.","productDescription":"5 p.","startPage":"4854","endPage":"4858","costCenters":[{"id":531,"text":"Patuxent Wildlife Research Center","active":true,"usgs":true}],"links":[{"id":477991,"rank":1,"type":{"id":41,"text":"Open Access External Repository Page"},"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/387338","text":"External Repository"},{"id":199448,"rank":0,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"}],"country":"India","geographicExtents":"{\n \"type\": \"FeatureCollection\",\n \"features\": [\n {\n \"type\": \"Feature\",\n \"properties\": {},\n \"geometry\": {\n \"type\": \"Polygon\",\n \"coordinates\": [\n [\n [\n 71.89453125,\n 29.38217507514529\n ],\n [\n 69.08203125,\n 27.21555620902969\n ],\n [\n 70.3125,\n 25.64152637306577\n ],\n [\n 69.08203125,\n 21.616579336740603\n ],\n [\n 70.3125,\n 20.138470312451155\n ],\n [\n 72.0703125,\n 19.973348786110602\n ],\n [\n 72.24609375,\n 17.811456088564483\n ],\n [\n 74.70703125,\n 11.867350911459308\n ],\n [\n 76.2890625,\n 7.18810087117902\n ],\n [\n 79.62890625,\n 8.407168163601076\n ],\n [\n 80.68359375,\n 11.867350911459308\n ],\n [\n 81.38671875,\n 14.944784875088372\n ],\n [\n 84.19921875,\n 16.97274101999902\n ],\n [\n 89.12109375,\n 22.755920681486405\n ],\n [\n 82.265625,\n 28.613459424004414\n ],\n [\n 79.98046875,\n 33.284619968887675\n ],\n [\n 74.35546875,\n 32.10118973232094\n ],\n [\n 71.89453125,\n 29.38217507514529\n ]\n ]\n ]\n }\n }\n ]\n}","volume":"101","issue":"14","noUsgsAuthors":false,"publicationDate":"2004-03-23","publicationStatus":"PW","scienceBaseUri":"4f4e4a53e4b07f02db62b6e8","contributors":{"authors":[{"text":"Karanth, K. U.","contributorId":23645,"corporation":false,"usgs":true,"family":"Karanth","given":"K.","email":"","middleInitial":"U.","affiliations":[],"preferred":false,"id":341199,"contributorType":{"id":1,"text":"Authors"},"rank":1},{"text":"Nichols, J.D. 0000-0002-7631-2890","orcid":"https://orcid.org/0000-0002-7631-2890","contributorId":14332,"corporation":false,"usgs":true,"family":"Nichols","given":"J.D.","affiliations":[],"preferred":false,"id":341197,"contributorType":{"id":1,"text":"Authors"},"rank":2},{"text":"Kumar, S.","contributorId":17714,"corporation":false,"usgs":true,"family":"Kumar","given":"S.","affiliations":[],"preferred":false,"id":341198,"contributorType":{"id":1,"text":"Authors"},"rank":3},{"text":"Link, W.A. 0000-0002-9913-0256","orcid":"https://orcid.org/0000-0002-9913-0256","contributorId":8815,"corporation":false,"usgs":true,"family":"Link","given":"W.A.","affiliations":[],"preferred":false,"id":341196,"contributorType":{"id":1,"text":"Authors"},"rank":4},{"text":"Hines, J.E. 0000-0001-5478-7230","orcid":"https://orcid.org/0000-0001-5478-7230","contributorId":36885,"corporation":false,"usgs":true,"family":"Hines","given":"J.E.","affiliations":[{"id":531,"text":"Patuxent Wildlife Research Center","active":true,"usgs":true}],"preferred":false,"id":341200,"contributorType":{"id":1,"text":"Authors"},"rank":5}]}} ,{"id":5224290,"text":"5224290 - 2004 - Monitoring programs need to take into account imperfect species detectability","interactions":[],"lastModifiedDate":"2012-02-02T00:15:37","indexId":"5224290","displayToPublicDate":"2010-06-16T12:18:50","publicationYear":"2004","noYear":false,"publicationType":{"id":2,"text":"Article"},"publicationSubtype":{"id":10,"text":"Journal Article"},"seriesTitle":{"id":970,"text":"Basic and Applied Ecology","active":true,"publicationSubtype":{"id":10}},"title":"Monitoring programs need to take into account imperfect species detectability","docAbstract":"Biodiversiry monitoring is important to identify biological units in need of conservation and to check the effectiveness of conservation actions. Programs generally monitor species richness and its changes (trend). Usually, no correction is made for imperfect species detectability. Instead, it is assumed that each species present has the same probability of being recorded and that there is no difference in this detectability across space and time, e.g. among observers and habitats. Consequently, species richness is determined by enumeration as the sum of species recorded. In Switzerland, the federal government has recently launched a comprehensive program that aims at detecting changes in biodiversity at all levels of biological integration. Birds are an important part of that program. Since 1999, 23 visits per breeding season are made to each of >250 1 km2 squares to map the territories of all detected breeding bird species. Here, we analyse data from three squares to illustrate the use of capture-recapture models in monitoring to obtain detectability-corrected estimates of species richness and trend. Species detectability averaged only 85%. Hence an estimated 15% of species present remained overlooked even after three visits. Within a square, changes in detectability for different years were of the same magnitude when surveys were conducted by the same observer as when they were by different observers. Estimates of trend were usually biased and community turnover was overestimated when based on enumeration. Here we use bird data as an illustration of methods. However, species detectability for any taxon is unlikely ever to be perfect or even constant across categories to be compared. Therefore, monitoring programs should correct for species detectability.","largerWorkType":{"id":2,"text":"Article"},"largerWorkTitle":"Basic and Applied Ecology","largerWorkSubtype":{"id":10,"text":"Journal Article"},"language":"English","doi":"10.1078/1439-1791-00194","collaboration":"6127_Kery.pdf","usgsCitation":"Kery, M., and Schmid, H., 2004, Monitoring programs need to take into account imperfect species detectability: Basic and Applied Ecology, v. 5, no. 1, p. 65-73, https://doi.org/10.1078/1439-1791-00194.","productDescription":"65-73","startPage":"65","endPage":"73","numberOfPages":"9","costCenters":[{"id":531,"text":"Patuxent Wildlife Research Center","active":true,"usgs":true}],"links":[{"id":199446,"rank":0,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"},{"id":17401,"rank":200,"type":{"id":11,"text":"Document"},"url":"https://dx.doi.org/10.1078/1439-1791-00194","linkFileType":{"id":5,"text":"html"}}],"volume":"5","issue":"1","noUsgsAuthors":false,"publicationStatus":"PW","scienceBaseUri":"4f4e4a61e4b07f02db6358cf","contributors":{"authors":[{"text":"Kery, M.","contributorId":46637,"corporation":false,"usgs":true,"family":"Kery","given":"M.","affiliations":[],"preferred":false,"id":341175,"contributorType":{"id":1,"text":"Authors"},"rank":1},{"text":"Schmid, Hans","contributorId":19648,"corporation":false,"usgs":true,"family":"Schmid","given":"Hans","affiliations":[],"preferred":false,"id":341174,"contributorType":{"id":1,"text":"Authors"},"rank":2}]}} ,{"id":5224623,"text":"5224623 - 2004 - Detecting warning signs of trouble within population fluctuations: using capture-recapture modeling to uncover changes in population dynamics leading to declines","interactions":[],"lastModifiedDate":"2012-02-02T00:15:32","indexId":"5224623","displayToPublicDate":"2010-06-16T12:18:50","publicationYear":"2004","noYear":false,"publicationType":{"id":2,"text":"Article"},"publicationSubtype":{"id":10,"text":"Journal Article"},"seriesTitle":{"id":803,"text":"Annual Meeting of the Association of Field Ornithologists and the Wilson Ornithological Society Program and Abstracts","active":true,"publicationSubtype":{"id":10}},"title":"Detecting warning signs of trouble within population fluctuations: using capture-recapture modeling to uncover changes in population dynamics leading to declines","docAbstract":"An intensive mark-recapture/resighting program has been carried out on the Roseate Terns nesting at Falkner Island, Connecticut, since the late 1980s as part of a regional study of the metapopulation dynamics and ecology of the endangered Northwest Atlantic breeding population of this species. Substantial losses of tern eggs and chicks to predation at this colony site began in 1996 when at least five Black-crowned Night-Herons started nocturnal raids. This depredation has been a major factor in the reduction of productivity from an average of about 1.0 chicks/pair for the 10 years before night-heron predation began to as low as about 0.2 chicks/pair in 2002. Recent capture-recapture modelling analyses have detected other important impacts on the population dynamics of the Roseate Terns at this site including a reduction by about half in the 'development-of-residency' rates of first-time breeders, and a substantial decline in the local 'survival-and-fidelity' rates of experienced breeders believed due mostly to increased immigration rates to other colony sites.","largerWorkType":{"id":2,"text":"Article"},"largerWorkTitle":"Annual Meeting of the Association of Field Ornithologists and the Wilson Ornithological Society Program and Abstracts","largerWorkSubtype":{"id":10,"text":"Journal Article"},"language":"English","collaboration":"Meeting held April 22-24, 2004 at the Cornell Laboratory of Ornithology, Ithaca, NY","usgsCitation":"Spendelow, J., Nichols, J., Kendall, W., Hines, J., Hatfield, J., and Nisbet, I., 2004, Detecting warning signs of trouble within population fluctuations: using capture-recapture modeling to uncover changes in population dynamics leading to declines: Annual Meeting of the Association of Field Ornithologists and the Wilson Ornithological Society Program and Abstracts.","productDescription":"P42","startPage":"P42","costCenters":[{"id":531,"text":"Patuxent Wildlife Research Center","active":true,"usgs":true}],"links":[{"id":201994,"rank":0,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"}],"noUsgsAuthors":false,"publicationStatus":"PW","scienceBaseUri":"4f4e4aa8e4b07f02db667ae4","contributors":{"authors":[{"text":"Spendelow, J. A. 0000-0001-8167-0898","orcid":"https://orcid.org/0000-0001-8167-0898","contributorId":72478,"corporation":false,"usgs":true,"family":"Spendelow","given":"J. A.","affiliations":[],"preferred":false,"id":342131,"contributorType":{"id":1,"text":"Authors"},"rank":1},{"text":"Nichols, J.D. 0000-0002-7631-2890","orcid":"https://orcid.org/0000-0002-7631-2890","contributorId":14332,"corporation":false,"usgs":true,"family":"Nichols","given":"J.D.","affiliations":[],"preferred":false,"id":342126,"contributorType":{"id":1,"text":"Authors"},"rank":2},{"text":"Kendall, W. L. 0000-0003-0084-9891","orcid":"https://orcid.org/0000-0003-0084-9891","contributorId":32880,"corporation":false,"usgs":true,"family":"Kendall","given":"W. L.","affiliations":[{"id":531,"text":"Patuxent Wildlife Research Center","active":true,"usgs":true}],"preferred":false,"id":342127,"contributorType":{"id":1,"text":"Authors"},"rank":3},{"text":"Hines, J.E. 0000-0001-5478-7230","orcid":"https://orcid.org/0000-0001-5478-7230","contributorId":36885,"corporation":false,"usgs":true,"family":"Hines","given":"J.E.","affiliations":[{"id":531,"text":"Patuxent Wildlife Research Center","active":true,"usgs":true}],"preferred":false,"id":342128,"contributorType":{"id":1,"text":"Authors"},"rank":4},{"text":"Hatfield, Jeff S.","contributorId":41372,"corporation":false,"usgs":true,"family":"Hatfield","given":"Jeff S.","affiliations":[],"preferred":false,"id":342129,"contributorType":{"id":1,"text":"Authors"},"rank":5},{"text":"Nisbet, I.C.T.","contributorId":54942,"corporation":false,"usgs":true,"family":"Nisbet","given":"I.C.T.","email":"","affiliations":[],"preferred":false,"id":342130,"contributorType":{"id":1,"text":"Authors"},"rank":6}]}} ,{"id":5224486,"text":"5224486 - 2004 - Sex Determination of Carolina Wrens (Thryothorus ludovicianus) in the Mississippi Alluvial Valley","interactions":[],"lastModifiedDate":"2012-02-02T00:15:10","indexId":"5224486","displayToPublicDate":"2010-06-16T12:18:39","publicationYear":"2004","noYear":false,"publicationType":{"id":2,"text":"Article"},"publicationSubtype":{"id":10,"text":"Journal Article"},"seriesTitle":{"id":2881,"text":"North American Bird Bander","active":true,"publicationSubtype":{"id":10}},"title":"Sex Determination of Carolina Wrens (Thryothorus ludovicianus) in the Mississippi Alluvial Valley","docAbstract":"I identified sexual dimorphism in wing length (unflattened chord) of Carolina Wrens (Thryothorus ludovicianus) within the central Mississippi Alluvial Valley (northeast Louisiana and west-central Mississippi) and used this difference to assign a sex to captured wrens. Wrens were identified as female when wing length was less than 57.5 mm or male when wing length was greater than 58.5 mm. Verification of predicted sex was obtained from recaptures of banded individuals where sex was ascertained from the presence of a cloacal protuberance or brood patch. Correct prediction of sex was 81% for adult females and 95% for adult males. An alternative model, which categorized wrens with wing lengths of 58 and 59 mm as birds of unknown sex, increased correct prediction of females to 93% but reduced the number of individuals to which sex was assigned. These simple, predictive, wing-length-based models also correctly assigned sex for more than 88% of young (hatching-year) birds.","largerWorkType":{"id":2,"text":"Article"},"largerWorkTitle":"North American Bird Bander","largerWorkSubtype":{"id":10,"text":"Journal Article"},"language":"English","collaboration":"6414_Twedt.pdf","usgsCitation":"Twedt, D., 2004, Sex Determination of Carolina Wrens (Thryothorus ludovicianus) in the Mississippi Alluvial Valley: North American Bird Bander, v. 29, no. 4, p. 171-174.","productDescription":"171-174","startPage":"171","endPage":"174","numberOfPages":"4","costCenters":[{"id":531,"text":"Patuxent Wildlife Research Center","active":true,"usgs":true}],"links":[{"id":196129,"rank":0,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"}],"volume":"29","issue":"4","noUsgsAuthors":false,"publicationStatus":"PW","scienceBaseUri":"4f4e49fbe4b07f02db5f4aed","contributors":{"authors":[{"text":"Twedt, D.J. 0000-0003-1223-5045","orcid":"https://orcid.org/0000-0003-1223-5045","contributorId":105009,"corporation":false,"usgs":true,"family":"Twedt","given":"D.J.","affiliations":[],"preferred":false,"id":341855,"contributorType":{"id":1,"text":"Authors"},"rank":1}]}} ,{"id":5224798,"text":"5224798 - 2004 - N-mixture models for estimating population size from spatially replicated counts","interactions":[],"lastModifiedDate":"2021-07-09T14:48:16.426439","indexId":"5224798","displayToPublicDate":"2010-06-16T12:18:39","publicationYear":"2004","noYear":false,"publicationType":{"id":2,"text":"Article"},"publicationSubtype":{"id":10,"text":"Journal Article"},"seriesTitle":{"id":1039,"text":"Biometrics","active":true,"publicationSubtype":{"id":10}},"title":"N-mixture models for estimating population size from spatially replicated counts","docAbstract":"Spatial replication is a common theme in count surveys of animals. Such surveys often generate sparse count data from which it is difficult to estimate population size while formally accounting for detection probability. In this article, I describe a class of models (n-mixture models) which allow for estimation of population size from such data. The key idea is to view site-specific population sizes, n, as independent random variables distributed according to some mixing distribution (e.g., Poisson). Prior parameters are estimated from the marginal likelihood of the data, having integrated over the prior distribution for n. Carroll and Lombard (1985, Journal of American Statistical Association 80, 423-426) proposed a class of estimators based on mixing over a prior distribution for detection probability. Their estimator can be applied in limited settings, but is sensitive to prior parameter values that are fixed a priori. Spatial replication provides additional information regarding the parameters of the prior distribution on n that is exploited by the n-mixture models and which leads to reasonable estimates of abundance from sparse data. A simulation study demonstrates superior operating characteristics (bias, confidence interval coverage) of the n-mixture estimator compared to the Caroll and Lombard estimator. Both estimators are applied to point count data on six species of birds illustrating the sensitivity to choice of prior on p and substantially different estimates of abundance as a consequence.
","language":"English","publisher":"Wiley Online Library","doi":"10.1111/j.0006-341X.2004.00142.x","usgsCitation":"Royle, J., 2004, N-mixture models for estimating population size from spatially replicated counts: Biometrics, v. 60, no. 1, p. 108-115, https://doi.org/10.1111/j.0006-341X.2004.00142.x.","productDescription":"8 p.","startPage":"108","endPage":"115","costCenters":[{"id":531,"text":"Patuxent Wildlife Research Center","active":true,"usgs":true}],"links":[{"id":477995,"rank":1,"type":{"id":40,"text":"Open Access Publisher Index Page"},"url":"https://doi.org/10.1111/j.0006-341x.2004.00142.x","text":"Publisher Index Page"},{"id":202036,"rank":0,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"}],"volume":"60","issue":"1","noUsgsAuthors":false,"publicationDate":"2004-03-11","publicationStatus":"PW","scienceBaseUri":"4f4e4b32e4b07f02db6b492c","contributors":{"authors":[{"text":"Royle, J. Andrew 0000-0003-3135-2167","orcid":"https://orcid.org/0000-0003-3135-2167","contributorId":96221,"corporation":false,"usgs":true,"family":"Royle","given":"J. Andrew","affiliations":[],"preferred":false,"id":342710,"contributorType":{"id":1,"text":"Authors"},"rank":1}]}} ,{"id":5224614,"text":"5224614 - 2004 - Modeling abundance effects in distance sampling","interactions":[],"lastModifiedDate":"2021-11-29T15:57:28.992797","indexId":"5224614","displayToPublicDate":"2010-06-16T12:18:39","publicationYear":"2004","noYear":false,"publicationType":{"id":2,"text":"Article"},"publicationSubtype":{"id":10,"text":"Journal Article"},"seriesTitle":{"id":1465,"text":"Ecology","active":true,"publicationSubtype":{"id":10}},"title":"Modeling abundance effects in distance sampling","docAbstract":"Distance-sampling methods are commonly used in studies of animal populations to estimate population density. A common objective of such studies is to evaluate the relationship between abundance or density and covariates that describe animal habitat or other environmental influences. However, little attention has been focused on methods of modeling abundance covariate effects in conventional distance-sampling models. In this paper we propose a distance-sampling model that accommodates covariate effects on abundance. The model is based on specification of the distance-sampling likelihood at the level of the sample unit in terms of local abundance (for each sampling unit). This model is augmented with a Poisson regression model for local abundance that is parameterized in terms of available covariates. Maximum-likelihood estimation of detection and density parameters is based on the integrated likelihood, wherein local abundance is removed from the likelihood by integration. We provide an example using avian point-transect data of Ovenbirds (Seiurus aurocapillus) collected using a distance-sampling protocol and two measures of habitat structure (understory cover and basal area of overstory trees). The model yields a sensible description (positive effect of understory cover, negative effect on basal area) of the relationship between habitat and Ovenbird density that can be used to evaluate the effects of habitat management on Ovenbird populations.
","language":"English","publisher":"Wiley","doi":"10.1890/03-3127","usgsCitation":"Royle, J., Dawson, D., and Bates, S., 2004, Modeling abundance effects in distance sampling: Ecology, v. 85, no. 6, p. 1591-1597, https://doi.org/10.1890/03-3127.","productDescription":"7 p.","startPage":"1591","endPage":"1597","costCenters":[{"id":531,"text":"Patuxent Wildlife Research Center","active":true,"usgs":true}],"links":[{"id":203204,"rank":0,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"}],"country":"United States","state":"Maryland","county":"Frederick County","otherGeospatial":"Catoctin Mountains","geographicExtents":"{\n \"type\": \"FeatureCollection\",\n \"features\": [\n {\n \"type\": \"Feature\",\n \"properties\": {},\n \"geometry\": {\n \"type\": \"Polygon\",\n \"coordinates\": [\n [\n [\n -77.5579833984375,\n 39.457402514270825\n ],\n [\n -77.40692138671875,\n 39.457402514270825\n ],\n [\n -77.40692138671875,\n 39.68605343225986\n ],\n [\n -77.5579833984375,\n 39.68605343225986\n ],\n [\n -77.5579833984375,\n 39.457402514270825\n ]\n ]\n ]\n }\n }\n ]\n}","volume":"85","issue":"6","noUsgsAuthors":false,"publicationStatus":"PW","scienceBaseUri":"4f4e4a29e4b07f02db611c93","contributors":{"authors":[{"text":"Royle, J. Andrew 0000-0003-3135-2167","orcid":"https://orcid.org/0000-0003-3135-2167","contributorId":96221,"corporation":false,"usgs":true,"family":"Royle","given":"J. Andrew","affiliations":[],"preferred":false,"id":342091,"contributorType":{"id":1,"text":"Authors"},"rank":1},{"text":"Dawson, D.K. 0000-0001-7531-212X","orcid":"https://orcid.org/0000-0001-7531-212X","contributorId":94752,"corporation":false,"usgs":true,"family":"Dawson","given":"D.K.","affiliations":[],"preferred":false,"id":342090,"contributorType":{"id":1,"text":"Authors"},"rank":2},{"text":"Bates, S.","contributorId":44271,"corporation":false,"usgs":true,"family":"Bates","given":"S.","email":"","affiliations":[],"preferred":false,"id":342089,"contributorType":{"id":1,"text":"Authors"},"rank":3}]}} ,{"id":5224395,"text":"5224395 - 2004 - Estimation of sex-specific survival from capture-recapture data when sex is not always known","interactions":[],"lastModifiedDate":"2021-08-13T16:05:38.772379","indexId":"5224395","displayToPublicDate":"2010-06-16T12:18:36","publicationYear":"2004","noYear":false,"publicationType":{"id":2,"text":"Article"},"publicationSubtype":{"id":10,"text":"Journal Article"},"seriesTitle":{"id":1465,"text":"Ecology","active":true,"publicationSubtype":{"id":10}},"title":"Estimation of sex-specific survival from capture-recapture data when sex is not always known","docAbstract":"Many animals lack obvious sexual dimorphism, making assignment of sex difficult even for observed or captured animals. For many such species it is possible to assign sex with certainty only at some occasions; for example, when they exhibit certain types of behavior. A common approach to handling this situation in capture-recapture studies has been to group capture histories into those of animals eventually identified as male and female and those for which sex was never known. Because group membership is dependent on the number of occasions at which an animal was caught or observed (known sex animals, on average, will have been observed at more occasions than unknown-sex animals), survival estimates for known-sex animals will be positively biased, and those for unknown animals will be negatively biased. In this paper, we develop capture-recapture models that incorporate sex ratio and sex assignment parameters that permit unbiased estimation in the face of this sampling problem. We demonstrate the magnitude of bias in the traditional capture-recapture approach to this sampling problem, and we explore properties of estimators from other ad hoc approaches. The model is then applied to capture-recapture data for adult Roseate Terns (Sterna dougallii) at Falkner Island, Connecticut, 1993-2002. Sex ratio among adults in this population favors females, and we tested the hypothesis that this population showed sex-specific differences in adult survival. Evidence was provided for higher survival of adult females than males, as predicted. We recommend use of this modeling approach for future capture-recapture studies in which sex cannot always be assigned to captured or observed animals. We also place this problem in the more general context of uncertainty in state classification in multistate capture-recapture models.
","language":"English","publisher":"Wiley","doi":"10.1890/03-0578","usgsCitation":"Nichols, J., Kendall, W., Hines, J., and Spendelow, J., 2004, Estimation of sex-specific survival from capture-recapture data when sex is not always known: Ecology, v. 85, no. 12, p. 3192-3201, https://doi.org/10.1890/03-0578.","productDescription":"10 p.","startPage":"3192","endPage":"3201","costCenters":[{"id":531,"text":"Patuxent Wildlife Research Center","active":true,"usgs":true}],"links":[{"id":201913,"rank":0,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"}],"country":"United States","state":"Connecticut","otherGeospatial":"Falkner Island","geographicExtents":"{\n \"type\": \"FeatureCollection\",\n \"features\": [\n {\n \"type\": \"Feature\",\n \"properties\": {},\n \"geometry\": {\n \"type\": \"Polygon\",\n \"coordinates\": [\n [\n [\n -72.65443325042725,\n 41.21288373722492\n ],\n [\n -72.65529155731201,\n 41.21217349004246\n ],\n [\n -72.65477657318114,\n 41.21152780409429\n ],\n [\n -72.65529155731201,\n 41.21052697828058\n ],\n [\n -72.65408992767334,\n 41.21059154814995\n ],\n [\n -72.65318870544434,\n 41.21152780409429\n ],\n [\n -72.65280246734618,\n 41.21201206915286\n ],\n [\n -72.65288829803467,\n 41.21327114152892\n ],\n [\n -72.6537036895752,\n 41.2136585435387\n ],\n [\n -72.65413284301756,\n 41.21352940979034\n ],\n [\n -72.65443325042725,\n 41.21288373722492\n ]\n ]\n ]\n }\n }\n ]\n}","volume":"85","issue":"12","noUsgsAuthors":false,"publicationStatus":"PW","scienceBaseUri":"4f4e4a0ae4b07f02db5fb1fa","contributors":{"authors":[{"text":"Nichols, J.D. 0000-0002-7631-2890","orcid":"https://orcid.org/0000-0002-7631-2890","contributorId":14332,"corporation":false,"usgs":true,"family":"Nichols","given":"J.D.","affiliations":[],"preferred":false,"id":341541,"contributorType":{"id":1,"text":"Authors"},"rank":1},{"text":"Kendall, W. 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A.","affiliations":[],"preferred":false,"id":341544,"contributorType":{"id":1,"text":"Authors"},"rank":4}]}} ,{"id":5224434,"text":"5224434 - 2004 - Generalized estimators of avian abundance from count survey data","interactions":[],"lastModifiedDate":"2016-10-27T12:08:11","indexId":"5224434","displayToPublicDate":"2010-06-16T12:18:29","publicationYear":"2004","noYear":false,"publicationType":{"id":2,"text":"Article"},"publicationSubtype":{"id":10,"text":"Journal Article"},"seriesTitle":{"id":771,"text":"Animal Biodiversity and Conservation","active":true,"publicationSubtype":{"id":10}},"title":"Generalized estimators of avian abundance from count survey data","docAbstract":"I consider modeling avian abundance from spatially referenced bird count data collected according to common protocols such as capture?recapture, multiple observer, removal sampling and simple point counts. Small sample sizes and large numbers of parameters have motivated many analyses that disregard the spatial indexing of the data, and thus do not provide an adequate treatment of spatial structure. I describe a general framework for modeling spatially replicated data that regards local abundance as a random process, motivated by the view that the set of spatially referenced local populations (at the sample locations) constitute a metapopulation. Under this view, attention can be focused on developing a model for the variation in local abundance independent of the sampling protocol being considered. The metapopulation model structure, when combined with the data generating model, define a simple hierarchical model that can be analyzed using conventional methods. The proposed modeling framework is completely general in the sense that broad classes of metapopulation models may be considered, site level covariates on detection and abundance may be considered, and estimates of abundance and related quantities may be obtained for sample locations, groups of locations, unsampled locations. Two brief examples are given, the first involving simple point counts, and the second based on temporary removal counts. Extension of these models to open systems is briefly discussed.","language":"English","publisher":"Museu de Ciencies Naturals de Barcelona","usgsCitation":"Royle, J., 2004, Generalized estimators of avian abundance from count survey data: Animal Biodiversity and Conservation, v. 27, no. 1, p. 375-386.","productDescription":"12 p.","startPage":"375","endPage":"386","numberOfPages":"12","costCenters":[{"id":531,"text":"Patuxent Wildlife Research Center","active":true,"usgs":true}],"links":[{"id":196077,"rank":0,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"},{"id":16751,"rank":300,"type":{"id":15,"text":"Index Page"},"url":"https://abc.museucienciesjournals.cat/volum-27-1-2004-abc/generalized-estimators-of-avian-abundance-from-count-survey-data/?lang=en","linkFileType":{"id":5,"text":"html"}}],"volume":"27","issue":"1","noUsgsAuthors":false,"publicationStatus":"PW","scienceBaseUri":"4f4e4b26e4b07f02db6afca2","contributors":{"authors":[{"text":"Royle, J. Andrew 0000-0003-3135-2167","orcid":"https://orcid.org/0000-0003-3135-2167","contributorId":96221,"corporation":false,"usgs":true,"family":"Royle","given":"J. Andrew","affiliations":[],"preferred":false,"id":341667,"contributorType":{"id":1,"text":"Authors"},"rank":1}]}} ,{"id":5224447,"text":"5224447 - 2004 - Effectiveness of a confinement strategy for reducing campsite impacts in Shenandoah National Park","interactions":[],"lastModifiedDate":"2021-08-18T17:05:25.964757","indexId":"5224447","displayToPublicDate":"2010-06-16T12:18:29","publicationYear":"2004","noYear":false,"publicationType":{"id":2,"text":"Article"},"publicationSubtype":{"id":10,"text":"Journal Article"},"seriesTitle":{"id":1531,"text":"Environmental Conservation","active":true,"publicationSubtype":{"id":10}},"title":"Effectiveness of a confinement strategy for reducing campsite impacts in Shenandoah National Park","docAbstract":"The expansion and proliferation of backcountry campsites is a persistent problem in many parks and protected areas. Shenandoah National Park (SNP) has one of the highest backcountry overnight use densities in the USA national parks system. SNP managers implemented a multi-option backcountry camping policy in 2000 that included camping containment with established campsites. These actions were intended to reduce the number of campsites and the area of camping disturbance at each site. This paper describes a longitudinal adaptive management assessment of the new campsite policies, applying quantitative measures of campsite conditions to evaluate the efficacy of management interventions. Physical campsite measurements combined with qualitative visitor interviews indicated SNP had successfully reduced the number of campsites and aggregate measures of camping-related disturbance in the Park, while minimizing the use of regulations, site facilities and staff resources. Implications for managers of other protected areas are that an established site camping policy can minimize camping disturbance, including the number and size of campsites, provided managers can sustain rehabilitation efforts to close and restore unneeded campsites. Experiential attributes, such as the potential for solitude, can also be manipulated through control over the selection of established campsites. Integrating resource and social science methods also provided a more holistic perspective on management policy assessments. Adaptive management research provided a timely evaluation of management success while facilitating effective modifications in response to unforeseen challenges. Conclusions regarding the effectiveness of a visitor impact containment strategy involving an established site camping option are offered.","language":"English","publisher":"Cambridge University Press","doi":"10.1017/S0376892904001602","usgsCitation":"Reid, S.E., and Marion, J., 2004, Effectiveness of a confinement strategy for reducing campsite impacts in Shenandoah National Park: Environmental Conservation, v. 31, no. 4, p. 274-282, https://doi.org/10.1017/S0376892904001602.","productDescription":"9 p.","startPage":"274","endPage":"282","costCenters":[{"id":531,"text":"Patuxent Wildlife Research Center","active":true,"usgs":true}],"links":[{"id":477997,"rank":1,"type":{"id":41,"text":"Open Access External Repository Page"},"url":"https://doi.org/10.1017/s0376892904001602","text":"External Repository"},{"id":201747,"rank":0,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"}],"country":"United States","state":"Virginia","otherGeospatial":"Shenandoah National Park","geographicExtents":"{\n \"type\": \"FeatureCollection\",\n \"features\": [\n {\n \"type\": \"Feature\",\n \"properties\": {},\n \"geometry\": {\n \"type\": \"Polygon\",\n \"coordinates\": [\n [\n [\n -78.59069824218749,\n 38.39979663000095\n ],\n [\n -78.33251953125,\n 38.39979663000095\n ],\n [\n -78.33251953125,\n 38.53849850597664\n ],\n [\n -78.59069824218749,\n 38.53849850597664\n ],\n [\n -78.59069824218749,\n 38.39979663000095\n ]\n ]\n ]\n }\n }\n ]\n}","volume":"31","issue":"4","noUsgsAuthors":false,"publicationDate":"2005-04-13","publicationStatus":"PW","scienceBaseUri":"4f4e4a4be4b07f02db625383","contributors":{"authors":[{"text":"Reid, S. E.","contributorId":88847,"corporation":false,"usgs":false,"family":"Reid","given":"S.","email":"","middleInitial":"E.","affiliations":[],"preferred":false,"id":341703,"contributorType":{"id":1,"text":"Authors"},"rank":1},{"text":"Marion, J. L. 0000-0003-2226-689X","orcid":"https://orcid.org/0000-0003-2226-689X","contributorId":10888,"corporation":false,"usgs":true,"family":"Marion","given":"J. L.","affiliations":[],"preferred":false,"id":341702,"contributorType":{"id":1,"text":"Authors"},"rank":2}]}} ,{"id":5224429,"text":"5224429 - 2004 - Individual heterogeneity and identifiability in capture-recapture models","interactions":[],"lastModifiedDate":"2016-10-27T12:09:47","indexId":"5224429","displayToPublicDate":"2010-06-16T12:18:29","publicationYear":"2004","noYear":false,"publicationType":{"id":2,"text":"Article"},"publicationSubtype":{"id":10,"text":"Journal Article"},"seriesTitle":{"id":771,"text":"Animal Biodiversity and Conservation","active":true,"publicationSubtype":{"id":10}},"title":"Individual heterogeneity and identifiability in capture-recapture models","docAbstract":"Individual heterogeneity in detection probabilities is a far more serious problem for capture-recapture modeling than has previously been recognized. In this note, I illustrate that population size is not an identifiable parameter under the general closed population mark-recapture model Mh. The problem of identifiability is obvious if the population includes individuals with pi = 0, but persists even when it is assumed that individual detection probabilities are bounded away from zero. Identifiability may be attained within parametric families of distributions for pi, but not among parametric families of distributions. Consequently, in the presence of individual heterogeneity in detection probability, capture-recapture analysis is strongly model dependent.
","language":"English","publisher":"Museu de Ciencies Naturals de Barcelona","usgsCitation":"Link, W., 2004, Individual heterogeneity and identifiability in capture-recapture models: Animal Biodiversity and Conservation, v. 27, no. 1, p. 87-91.","productDescription":"5 p.","startPage":"87","endPage":"91","numberOfPages":"5","costCenters":[{"id":531,"text":"Patuxent Wildlife Research Center","active":true,"usgs":true}],"links":[{"id":196031,"rank":0,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"},{"id":16746,"rank":300,"type":{"id":15,"text":"Index Page"},"url":"https://abc.museucienciesjournals.cat/volum-27-1-2004-abc/individual-heterogeneity-and-identifiability-in-capture-recapture-models/?lang=en","linkFileType":{"id":5,"text":"html"}}],"volume":"27","issue":"1","noUsgsAuthors":false,"publicationStatus":"PW","scienceBaseUri":"4f4e477ee4b07f02db481236","contributors":{"authors":[{"text":"Link, W.A. 0000-0002-9913-0256","orcid":"https://orcid.org/0000-0002-9913-0256","contributorId":8815,"corporation":false,"usgs":true,"family":"Link","given":"W.A.","affiliations":[],"preferred":false,"id":341658,"contributorType":{"id":1,"text":"Authors"},"rank":1}]}} ,{"id":5224430,"text":"5224430 - 2004 - Computing and software","interactions":[],"lastModifiedDate":"2016-10-27T12:02:10","indexId":"5224430","displayToPublicDate":"2010-06-16T12:18:29","publicationYear":"2004","noYear":false,"publicationType":{"id":2,"text":"Article"},"publicationSubtype":{"id":10,"text":"Journal Article"},"seriesTitle":{"id":771,"text":"Animal Biodiversity and Conservation","active":true,"publicationSubtype":{"id":10}},"title":"Computing and software","docAbstract":"The reality is that the statistical methods used for analysis of data depend upon the availability of software. Analysis of marked animal data is no different than the rest of the statistical field. The methods used for analysis are those that are available in reliable software packages. Thus, the critical importance of having reliable, up–to–date software available to biologists is obvious. Statisticians have continued to develop more robust models, ever expanding the suite of potential analysis methods
available. But without software to implement these newer methods, they will languish in the abstract, and not be applied to the problems deserving them.
In the Computers and Software Session, two new software packages are described, a comparison of implementation of methods for the estimation of nest survival is provided, and a more speculative paper about how the next generation of software might be structured is presented.
Rotella et al. (2004) compare nest survival estimation with different software packages: SAS logistic regression, SAS non–linear mixed models, and Program MARK. Nests are assumed to be visited at various, possibly infrequent, intervals. All of the approaches described compute nest survival with the same likelihood, and require that the age of the nest is known to account for nests that eventually hatch. However, each approach offers advantages and disadvantages, explored by Rotella et al. (2004).
Efford et al. (2004) present a new software package called DENSITY. The package computes population abundance and density from trapping arrays and other detection methods with a new and unique approach. DENSITY represents the first major addition to the analysis of trapping arrays in 20 years.
Barker & White (2004) discuss how existing software such as Program MARK require that each new model’s likelihood must be programmed specifically for that model. They wishfully think that future software might allow the user to combine pieces of likelihood functions together to generate estimates. The idea is interesting, and maybe some bright young statistician can work out the specifics to implement the procedure.
Choquet et al. (2004) describe MSURGE, a software package that implements the multistate capture–recapture models. The unique feature of MSURGE is that the design matrix is constructed with an interpreted language called GEMACO. Because MSURGE is limited to just multistate models, the special requirements of these likelihoods can be provided.
The software and methods presented in these papers gives biologists and wildlife managers an expanding range of possibilities for data analysis. Although ease–of–use is generally getting better, it does not replace the need for understanding of the requirements and structure of the models being computed. The internet provides access to many free software packages as well as user–discussion groups to share knowledge and ideas. (A starting point for wildlife–related applications is (http://www.phidot.org).
The EURING meetings and the scientists who have attended them have contributed substantially to the growth of knowledge in the field of estimating parameters of animal populations. The contributions of David R. Anderson to process modeling, parameter estimation and decision analysis are briefly reviewed. Metrics are considered for assessing individual contributions to a field of inquiry, and it is concluded that Anderson’s contributions have been substantial. Important characteristics of Anderson and his career are the ability to identify and focus on important topics, the premium placed on dissemination of new methods to prospective users, the ability to assemble teams of complementary researchers, and the innovation and vision that characterized so much of his work. The paper concludes with a list of interesting current research topics for consideration by EURING participants.
","language":"English","publisher":"Museu de Ciencies Natural de Barcelona","usgsCitation":"Nichols, J., 2004, Evolution of quantitative methods for the study and management of avian populations: on the importance of individual contributions: Animal Biodiversity and Conservation, v. 27, no. 1, p. 3-19.","productDescription":"17 p.","startPage":"3","endPage":"19","numberOfPages":"17","costCenters":[{"id":531,"text":"Patuxent Wildlife Research Center","active":true,"usgs":true}],"links":[{"id":201976,"rank":0,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"},{"id":16748,"rank":2,"type":{"id":15,"text":"Index Page"},"url":"https://abc.museucienciesjournals.cat/volum-27-1-2004-abc/evolution-of-quantitative-methods-for-the-study-and-management-of-avian-populations-on-the-importance-of-individual-contributions/?lang=en","linkFileType":{"id":5,"text":"html"}}],"volume":"27","issue":"1","noUsgsAuthors":false,"publicationStatus":"PW","scienceBaseUri":"4f4e49e2e4b07f02db5e4e22","contributors":{"authors":[{"text":"Nichols, J.D. 0000-0002-7631-2890","orcid":"https://orcid.org/0000-0002-7631-2890","contributorId":14332,"corporation":false,"usgs":true,"family":"Nichols","given":"J.D.","affiliations":[],"preferred":false,"id":341661,"contributorType":{"id":1,"text":"Authors"},"rank":1}]}} ,{"id":5224433,"text":"5224433 - 2004 - Costs of detection bias in index-based population monitoring","interactions":[],"lastModifiedDate":"2016-10-27T11:57:14","indexId":"5224433","displayToPublicDate":"2010-06-16T12:18:29","publicationYear":"2004","noYear":false,"publicationType":{"id":2,"text":"Article"},"publicationSubtype":{"id":10,"text":"Journal Article"},"seriesTitle":{"id":771,"text":"Animal Biodiversity and Conservation","active":true,"publicationSubtype":{"id":10}},"title":"Costs of detection bias in index-based population monitoring","docAbstract":"Managers of wildlife populations commonly rely on indirect, count-based measures of the population in making decisions regarding conservation, harvest, or control. The main appeal in the use of such counts is their low material expense compared to methods that directly measure the population. However, their correct use rests on the rarely-tested but often-assumed premise that they proportionately reflect population size, i.e., that they constitute a population index. This study investigates forest management for the endangered Red-cockaded Woodpecker (Picoides borealis) and the Wood Thrush (Hylocichla mustelina) at the Piedmont National Wildlife Refuge in central Georgia, U.S.A. Optimal decision policies for a joint species objective were derived for two alternative models of Wood Thrush population dynamics. Policies were simulated under scenarios of unbiasedness, consistent negative bias, and habitat-dependent negative bias in observed Wood Thrush densities. Differences in simulation outcomes between biased and unbiased detection scenarios indicated the expected loss in resource objectives (here, forest habitat and birds) through decision-making based on biased population counts. Given the models and objective function used in our analysis, expected losses were as great as 11%, a degree of loss perhaps not trivial for applications such as endangered species management. Our analysis demonstrates that costs of uncertainty about the relationship between the population and its observation can be measured in units of the resource, costs which may offset apparent savings achieved by collecting uncorrected population counts.","language":"English","publisher":"Museu de Ciencies Naturals de Barcelona","usgsCitation":"Moore, C., and Kendall, W., 2004, Costs of detection bias in index-based population monitoring: Animal Biodiversity and Conservation, v. 27, no. 1, p. 287-296.","productDescription":"10 p.","startPage":"287","endPage":"296","numberOfPages":"10","costCenters":[{"id":531,"text":"Patuxent Wildlife Research Center","active":true,"usgs":true}],"links":[{"id":202028,"rank":0,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"},{"id":16750,"rank":300,"type":{"id":15,"text":"Index Page"},"url":"https://abc.museucienciesjournals.cat/volum-27-1-2004-abc/costs-of-detection-bias-in-index-ased-population-monitoring/?lang=en","linkFileType":{"id":5,"text":"html"}}],"volume":"27","issue":"1","noUsgsAuthors":false,"publicationStatus":"PW","scienceBaseUri":"4f4e4ad5e4b07f02db68385b","contributors":{"authors":[{"text":"Moore, C. T. 0000-0002-6053-2880","orcid":"https://orcid.org/0000-0002-6053-2880","contributorId":87649,"corporation":false,"usgs":true,"family":"Moore","given":"C. T.","affiliations":[{"id":531,"text":"Patuxent Wildlife Research Center","active":true,"usgs":true}],"preferred":true,"id":341666,"contributorType":{"id":1,"text":"Authors"},"rank":1},{"text":"Kendall, W. L. 0000-0003-0084-9891","orcid":"https://orcid.org/0000-0003-0084-9891","contributorId":32880,"corporation":false,"usgs":true,"family":"Kendall","given":"W. L.","affiliations":[{"id":531,"text":"Patuxent Wildlife Research Center","active":true,"usgs":true}],"preferred":false,"id":341665,"contributorType":{"id":1,"text":"Authors"},"rank":2}]}} ,{"id":5224435,"text":"5224435 - 2004 - Abundance estimation and conservation biology","interactions":[],"lastModifiedDate":"2016-10-27T12:06:27","indexId":"5224435","displayToPublicDate":"2010-06-16T12:18:29","publicationYear":"2004","noYear":false,"publicationType":{"id":2,"text":"Article"},"publicationSubtype":{"id":10,"text":"Journal Article"},"seriesTitle":{"id":771,"text":"Animal Biodiversity and Conservation","active":true,"publicationSubtype":{"id":10}},"title":"Abundance estimation and conservation biology","docAbstract":"Abundance is the state variable of interest in most population–level ecological research and in most programs involving management and conservation of animal populations. Abundance is the single parameter of interest in capture–recapture models for closed populations (e.g., Darroch, 1958; Otis et al., 1978; Chao, 2001). The initial capture–recapture models developed for partially (Darroch, 1959) and completely (Jolly, 1965; Seber, 1965) open populations represented efforts to relax the restrictive assumption of population closure for the purpose of estimating abundance. Subsequent emphases in capture–recapture work were on survival rate estimation in the 1970’s and 1980’s (e.g., Burnham et al., 1987; Lebreton et al.,1992), and on movement estimation in the 1990’s (Brownie et al., 1993; Schwarz et al., 1993). However, from the mid–1990’s until the present time, capture–recapture investigators have expressed a renewed interest in abundance and related parameters (Pradel, 1996; Schwarz & Arnason, 1996; Schwarz, 2001). The focus of this session was abundance, and presentations covered topics ranging from estimation of abundance and rate of change in abundance, to inferences about the demographic processes underlying changes in abundance, to occupancy as a surrogate of abundance. The plenary paper by Link & Barker (2004) is provocative and very interesting, and it contains a number of important messages and suggestions. Link & Barker (2004) emphasize that the increasing complexity of capture–recapture models has resulted in large numbers of parameters and that a challenge to ecologists is to extract ecological signals from this complexity. They offer hierarchical models as a natural approach to inference in which traditional parameters are viewed as realizations of stochastic processes. These processes are governed by hyperparameters, and the inferential approach focuses on these hyperparameters. Link & Barker (2004) also suggest that our attention should be focused on relationships between demographic processes such as survival and recruitment, the two quantities responsible for changes in abundance, rather than simply on the magnitudes of these quantities. They describe a type of Jolly–Seber capture–recapture model that permits inference about the underlying relationship between per capita recruitment rates and survival rates (Link & Barker, this volume). Implementation used Bayesian Markov Chain Monte Carlo methods and appeared to work well, yielding inferences about the relationship between recruitment and survival that were robust to selection of prior distribution. We believe that readers will find their arguments compelling, and we expect to see increased use of hierarchical modeling approaches in capture–recapture and related fields. Otto (presentation without paper) also recommended use of hierarchical models in analysis of multiple data sources dealing with population dynamics of North American mallards. He integrated survival inferences from ringing data, abundance information from aerial survey data, and recruitment information based on age ratios from a harvest survey. He used a Leslie matrix population projection model as an integrating framework and obtained estimates of breeding population size using all data.Otto’s approach also permitted inference about biases in estimated quantities. As with the work of Link & Barker (2004), we find Otto’s recommendation to use hierarchical models to integrate data from multiple sources to be very compelling. Alisauskas et al. (2004) report results of an analysis of capture–recapture data for a askatchewan population of white–winged scoters. They used the approach of Pradel (1996) to estimate population growth rate (See the PDF) directly. Estimates for 1975–1985 were quite low, but estimates for the recent period, 2000–2003,increased to values > 1. Parameter estimates for seniority, survival and per capita recruitment (Pradel, 1996) led to the inference that increased recruitment was largely responsible for the improvements in population status and growth. However, various data sources also indicated that this increase in recruitment was likely a result of increased immigration rather than improved reproduction on the area. This latter inference is important from a conservation perspective in indicating the importance of birds in other locations to growth and health of the study population. Lukacs and Burnham presented material to be published elsewhere that dealt with the use of genetic markers in capture–recapture studies. The data sources for such studies are samples of hair or feces, which are then analyzed using molecular genetic techniques in order to determine individual genotypes with respect to a usually small number of loci. Two types of classification error can arise in such analyses. First, if only a small number of loci is examined, then there may be nonnegligible probabilities that multiple individual animals will have the same genotypes. The second type of error arises during the polymerase chain reaction (PCR) process and can result from failure of alleles to amplify (allelic dropout) or from PCR inhibitors in hair and feces that produce the appearance of false alleles or misprinting (Creel et al., 2003). Lukacs and Burnham developed models that formally incorporate possible misclassification of samples resulting from these errors. These models permit estimation of parameters such as abundance and survival in a manner that properly incorporates this uncertainty of individual identity. We anticipate that noninvasive sampling based on molecular genetic analyses of hair or feces will become extremely important for some species, and that the models of Lukacs and Burnham will become very popular for such analyses. MacKenzie & Nichols (2004) discuss the use of occupancy (proportion of patches or habitat area that is occupied) as a surrogate for abundance. In cases of territorial species and where birds occur at low densities, the number of occupied patches may provide a reasonable estimate of abundance. In other cases, occupancy can be viewed as providing information about one tail of the abundance distribution, P (N = 0). The motivation for considering occupancy as a surrogate for abundance is that occupancy is based on so–called presence–absence surveys that are frequently less expensive of time and effort than methods that estimate abundance directly. We describe one set of models that can be used to estimate occupancy for a single season and another that can be used to estimate parameters such as local probabilities of extinction and colonization that are associated with occupancy dynamics. We outline a possible hybrid approach that combines occupancy data with data on marked individuals in order to betterexplore the mechanisms underlying occupancy dynamics. These five presentations made for an interesting session containing useful information and recommendations for future work. A number of themes connecting these presentations could be emphasized. For example, two of the presentations considered alternatives to standard capture–recapture sampling that can be used to draw inferences about abundance, or a portion of the abundance distribution, with field methods that should be less expensive than usual capture–recapture approaches of handling animals. We believe that the most important theme of the session was the emphasis on the processes responsible for changes in abundance. In particular, we are excited by the potential for using hierarchical models as a means of investigating relationships among vital rates and as a means of combining multiple sources of data relevant to system dynamics. Indeed, we expect the importance of this session theme to be reflected in the content and presentations of the next EURING meeting.
","language":"English","publisher":"Museu de Ciencies Naturals de Barcelona","usgsCitation":"Nichols, J., and MacKenzie, D., 2004, Abundance estimation and conservation biology: Animal Biodiversity and Conservation, v. 27, no. 1, p. 437-439.","productDescription":"3 p.","startPage":"437","endPage":"439","numberOfPages":"3","costCenters":[{"id":531,"text":"Patuxent Wildlife Research Center","active":true,"usgs":true}],"links":[{"id":196327,"rank":0,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"},{"id":16752,"rank":300,"type":{"id":15,"text":"Index Page"},"url":"https://abc.museucienciesjournals.cat/volum-27-1-2004-abc/abundance-estimation-and-conservation-biology/?lang=en","linkFileType":{"id":5,"text":"html"}}],"volume":"27","issue":"1","noUsgsAuthors":false,"publicationStatus":"PW","scienceBaseUri":"4f4e4b13e4b07f02db6a3808","contributors":{"authors":[{"text":"Nichols, J.D. 0000-0002-7631-2890","orcid":"https://orcid.org/0000-0002-7631-2890","contributorId":14332,"corporation":false,"usgs":true,"family":"Nichols","given":"J.D.","affiliations":[],"preferred":false,"id":341668,"contributorType":{"id":1,"text":"Authors"},"rank":1},{"text":"MacKenzie, D.I.","contributorId":69522,"corporation":false,"usgs":true,"family":"MacKenzie","given":"D.I.","email":"","affiliations":[],"preferred":false,"id":341669,"contributorType":{"id":1,"text":"Authors"},"rank":2}]}} ]}