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Lemos Barão-Nóbrega JA, González-Jaurégui M, Jehle R. N-mixture models provide informative crocodile ( Crocodylus moreletii) abundance estimates in dynamic environments. PeerJ 2022; 10:e12906. [PMID: 35341055 PMCID: PMC8944345 DOI: 10.7717/peerj.12906] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 01/17/2022] [Indexed: 01/11/2023] Open
Abstract
Estimates of animal abundance provide essential information for population ecological studies. However, the recording of individuals in the field can be challenging, and accurate estimates require analytical techniques which account for imperfect detection. Here, we quantify local abundances and overall population size of Morelet's crocodiles (Crocodylus moreletii) in the region of Calakmul (Campeche, Mexico), comparing traditional approaches for crocodylians (Minimum Population Size-MPS; King's Visible Fraction Method-VFM) with binomial N-mixture models based on Poisson, zero-inflated Poisson (ZIP) and negative binomial (NB) distributions. A total of 191 nocturnal spotlight surveys were conducted across 40 representative locations (hydrologically highly dynamic aquatic sites locally known as aguadas) over a period of 3 years (2017-2019). Local abundance estimates revealed a median of 1 both through MPS (min-max: 0-89; first and third quartiles, Q1-Q3: 0-7) and VFM (0-112; Q1-Q3: 0-9) non-hatchling C. moreletii for each aguada, respectively. The ZIP based N-mixture approach shown overall superior confidence over Poisson and NB, and revealed a median of 6 ± 3 individuals (min = 0; max = 120 ± 18; Q1 = 0; Q3 = 18 ± 4) jointly with higher detectabilities in drying aguadas with low and intermediate vegetation cover. Extrapolating these inferences across all waterbodies in the study area yielded an estimated ~10,000 (7,000-11,000) C. moreletii present, highlighting Calakmul as an important region for this species. Because covariates enable insights into population responses to local environmental conditions, N-mixture models applied to spotlight count data result in particularly insightful estimates of crocodylian detection and abundance.
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Affiliation(s)
- José António Lemos Barão-Nóbrega
- Operation Wallacea, Spilsby, Lincolnshire, United Kingdom,School of Science, Engineering and Environment, University of Salford, Salford, Greater Manchester, United Kingdom
| | - Mauricio González-Jaurégui
- Universidad Autónoma de Campeche, Centro de Estudios de Desarrollo Sustentable y Aprovechamiento de la Vida Silvestre, Campeche, Campeche, Mexico
| | - Robert Jehle
- School of Science, Engineering and Environment, University of Salford, Salford, Greater Manchester, United Kingdom
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Sharma SP, Ghazi MG, Katdare S, Dasgupta N, Mondol S, Gupta SK, Hussain SA. Microsatellite analysis reveals low genetic diversity in managed populations of the critically endangered gharial (Gavialis gangeticus) in India. Sci Rep 2021; 11:5627. [PMID: 33707622 PMCID: PMC7970970 DOI: 10.1038/s41598-021-85201-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 02/25/2021] [Indexed: 01/31/2023] Open
Abstract
The gharial (Gavialis gangeticus) is a critically endangered crocodylian, endemic to the Indian subcontinent. The species has experienced severe population decline during the twentieth century owing to habitat loss, poaching, and mortalities in passive fishing. Its extant populations have largely recovered through translocation programmes initiated in 1975. Understanding the genetic status of these populations is crucial for evaluating the effectiveness of the ongoing conservation efforts. This study assessed the genetic diversity, population structure, and evidence of genetic bottlenecks of the two managed populations inhabiting the Chambal and Girwa Rivers, which hold nearly 80% of the global gharial populations. We used seven polymorphic nuclear microsatellite loci and a 520 bp partial fragment of the mitochondrial control region (CR). The overall mean allelic richness (Ar) was 2.80 ± 0.40, and the observed (Ho) and expected (He) heterozygosities were 0.40 ± 0.05 and 0.39 ± 0.05, respectively. We observed low levels of genetic differentiation between populations (FST = 0.039, P < 0.05; G'ST = 0.058, P < 0.05 Jost's D = 0.016, P < 0.05). The bottleneck analysis using the M ratio (Chambal = 0.31 ± 0.06; Girwa = 0.41 ± 0.12) suggested the presence of a genetic bottleneck in both populations. The mitochondrial CR also showed a low level of variation, with two haplotypes observed in the Girwa population. This study highlights the low level of genetic diversity in the two largest managed gharial populations in the wild. Hence, it is recommended to assess the genetic status of extant wild and captive gharial populations for planning future translocation programmes to ensure long-term survival in the wild.
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Affiliation(s)
- Surya Prasad Sharma
- Wildlife Institute of India, Chandrabani, P.O. Box # 18, Dehra Dun, Uttarakhand, 248002, India
| | | | - Suyash Katdare
- Wildlife Institute of India, Chandrabani, P.O. Box # 18, Dehra Dun, Uttarakhand, 248002, India
| | - Niladri Dasgupta
- Wildlife Institute of India, Chandrabani, P.O. Box # 18, Dehra Dun, Uttarakhand, 248002, India
| | - Samrat Mondol
- Wildlife Institute of India, Chandrabani, P.O. Box # 18, Dehra Dun, Uttarakhand, 248002, India
| | - Sandeep Kumar Gupta
- Wildlife Institute of India, Chandrabani, P.O. Box # 18, Dehra Dun, Uttarakhand, 248002, India
| | - Syed Ainul Hussain
- Wildlife Institute of India, Chandrabani, P.O. Box # 18, Dehra Dun, Uttarakhand, 248002, India.
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Neupane B, Singh BK, Poudel P, Panthi S, Khatri ND. Habitat occupancy and threat assessment of gharial (Gavialis gangeticus) in the Rapti River, Nepal. Glob Ecol Conserv 2020. [DOI: 10.1016/j.gecco.2020.e01270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
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The effectiveness of microsatellite DNA as a genetic tool in crocodilian conservation. CONSERV GENET RESOUR 2020. [DOI: 10.1007/s12686-020-01164-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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Augustine BC, Royle JA, Kelly MJ, Satter CB, Alonso RS, Boydston EE, Crooks KR. Spatial capture–recapture with partial identity: An application to camera traps. Ann Appl Stat 2018. [DOI: 10.1214/17-aoas1091] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Acharya KP, Khadka BK, Jnawali SR, Malla S, Bhattarai S, Wikramanayake E, Köhl M. Conservation and Population Recovery of Gharials (Gavialis gangeticus) in Nepal. HERPETOLOGICA 2017. [DOI: 10.1655/herpetologica-d-16-00048.1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Krishna Prasad Acharya
- Department of National Parks and Wildlife Conservation, Ministry of Forests and Soil Conservation, Kathmandu, Nepal
| | | | | | - Sabita Malla
- World Wildlife Fund Nepal Program, Kathmandu, Nepal
| | | | | | - Michael Köhl
- University of Hamburg, World Forestry, Hamburg, Germany
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Bouwman H, Cronje E. An 11-digit identification system for individual Nile crocodiles using natural markings. KOEDOE: AFRICAN PROTECTED AREA CONSERVATION AND SCIENCE 2016. [DOI: 10.4102/koedoe.v58i1.1351] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Abstract
Research and conservation of wild crocodiles and husbandry of captive crocodiles requires the reliable identification of individuals. We present a method using the individual colour markings on the first 10 single-crest scutes on the tails of Nile crocodiles (Crocodylus niloticus). The scutes are scored by number for colour, with a prefix for left or right providing a binary 11-digit identification number (identification numbers [IDs]; e.g. 12232232242 and 22333233232) per crocodile. A survey of 359 captive Nile crocodiles showed no duplication. However, 42% had asymmetrical scute markings requiring a binary approach. There does not seem to be a change in patterns with age, except that the number of missing scutes increased. A small trial showed that this method can be applied in the field, although more work is needed to determine observer bias and establish parameters for observability in the field. It is unlikely that both left and right IDs would be obtainable for each individual, but other distinctive markings such as scute shape and damage can be used to register the two IDs to one individual. Having two independent IDs for each crocodile provides the possibility of two independent population estimates for equal effort without having to link left and right IDs to individuals. Our proposed method would be useful in conservation, individual tracking and husbandry.Conservation implications: A non-invasive marking and recapture method for Nile crocodile is presented whereby the first 10 single-crest scutes are scored for colour, allowing conservation practitioners to count and monitor crocodile populations and individuals. This method provides two equal-effort estimations of population size, as left and right hand sides are scored independently.Keywords: Crocodylus niloticus; identification; mark - recapture; mark - resight
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McClintock BT. multimark: an R package for analysis of capture-recapture data consisting of multiple "noninvasive" marks. Ecol Evol 2015; 5:4920-31. [PMID: 26640671 PMCID: PMC4662319 DOI: 10.1002/ece3.1676] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Revised: 07/27/2015] [Accepted: 07/30/2015] [Indexed: 11/11/2022] Open
Abstract
I describe an open‐source R package, multimark, for estimation of survival and abundance from capture–mark–recapture data consisting of multiple “noninvasive” marks. Noninvasive marks include natural pelt or skin patterns, scars, and genetic markers that enable individual identification in lieu of physical capture. multimark provides a means for combining and jointly analyzing encounter histories from multiple noninvasive sources that otherwise cannot be reliably matched (e.g., left‐ and right‐sided photographs of bilaterally asymmetrical individuals). The package is currently capable of fitting open population Cormack–Jolly–Seber (CJS) and closed population abundance models with up to two mark types using Bayesian Markov chain Monte Carlo (MCMC) methods. multimark can also be used for Bayesian analyses of conventional capture–recapture data consisting of a single‐mark type. Some package features include (1) general model specification using formulas already familiar to most R users, (2) ability to include temporal, behavioral, age, cohort, and individual heterogeneity effects in detection and survival probabilities, (3) improved MCMC algorithm that is computationally faster and more efficient than previously proposed methods, (4) Bayesian multimodel inference using reversible jump MCMC, and (5) data simulation capabilities for power analyses and assessing model performance. I demonstrate use of multimark using left‐ and right‐sided encounter histories for bobcats (Lynx rufus) collected from remote single‐camera stations in southern California. In this example, there is evidence of a behavioral effect (i.e., trap “happy” response) that is otherwise indiscernible using conventional single‐sided analyses. The package will be most useful to ecologists seeking stronger inferences by combining different sources of mark–recapture data that are difficult (or impossible) to reliably reconcile, particularly with the sparse datasets typical of rare or elusive species for which noninvasive sampling techniques are most commonly employed. Addressing deficiencies in currently available software, multimark also provides a user‐friendly interface for performing Bayesian multimodel inference using capture–recapture data consisting of a single conventional mark or multiple noninvasive marks.
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Affiliation(s)
- Brett T McClintock
- National Marine Mammal Laboratory Alaska Fisheries Science Center NOAA-NMFS 7600 Sand Point Way NE Seattle Washington 98115
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McClintock BT, Conn PB, Alonso RS, Crooks KR. Integrated modeling of bilateral photo-identification data in mark–recapture analyses. Ecology 2013; 94:1464-71. [DOI: 10.1890/12-1613.1] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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