Subtopic Deep Dive

Capture-Recapture Models for Marine Populations
Research Guide

What is Capture-Recapture Models for Marine Populations?

Capture-Recapture Models for Marine Populations apply mark-recapture and photo-ID techniques to estimate abundance in elusive marine species, accounting for tag loss, temporary emigration, and multisite movements.

These models extend Lincoln-Petersen estimators to multi-event frameworks for mobile marine animals like whales and sharks. Photo-ID serves as natural marking for species such as humpback whales (Baker et al., 2013, 196 citations). Passive acoustics complement sightings for density estimation (Marques et al., 2012, 697 citations). Over 50 papers address marine applications since 2000.

Curated Papers

Key Challenges

Why It Matters

Accurate abundance estimates inform IUCN Red List assessments for baleen whales (Thomas et al., 2015, 207 citations). They guide bycatch mitigation in gillnet fisheries affecting marine mammals (Reeves et al., 2012, 385 citations). Population models support conservation amid climate-driven habitat shifts (Grémillet and Boulinier, 2009, 285 citations; Santora et al., 2020, 255 citations). Shark population sizes at reefs aid tourism and fishery management (Meekan et al., 2006, 194 citations).

Key Research Challenges

Tag Loss and Emigration

Marine tags detach due to fouling or behavior, biasing recapture rates (Hazen et al., 2012, 193 citations). Temporary emigration from study areas violates closure assumptions in mobile species like blue whales (Bailey et al., 2009, 238 citations). Multi-event models address these but require extensive data.

Multisite Population Movement

Animals move between sampling sites, complicating abundance estimation across regions (Bailey et al., 2009). Maternal fidelity structures populations, as in North Pacific humpbacks (Baker et al., 2013). State-space models integrate satellite tracks to model movements.

Low Detection in Elusive Species

Passive acoustics improve detection for density estimates in cetaceans (Marques et al., 2012, 697 citations). Photo-ID matching errors arise from poor image quality in sharks and whales (Meekan et al., 2006). Deep neural networks automate detection but need training data (Shiu et al., 2020, 194 citations).

Essential Papers

Estimating animal population density using passive acoustics

Tiago A. Marques, Len Thomas, Stephen W. Martin et al. · 2012 · Biological reviews/Biological reviews of the Cambridge Philosophical Society · 697 citations

ABSTRACT Reliable estimation of the size or density of wild animal populations is very important for effective wildlife management, conservation and ecology. Currently, the most widely used methods...

Marine mammal bycatch in gillnet and other entangling net fisheries, 1990 to 2011

RR Reeves, Kate McClellan, Thiemo Werner · 2012 · Endangered Species Research · 385 citations

Since the 1970s the role of fishery bycatch as a factor reducing, or limiting the recovery of, marine mammal populations has been increasingly recognized. The proceedings of a 1990 International Wh...

Spatial ecology and conservation of seabirds facing global climate change: a review

David Grémillet, Thierry Boulinier · 2009 · Marine Ecology Progress Series · 285 citations

MEPS Marine Ecology Progress Series Contact the journal Facebook Twitter RSS Mailing List Subscribe to our mailing list via Mailchimp HomeLatest VolumeAbout the JournalEditorsTheme Sections MEPS 39...

Habitat compression and ecosystem shifts as potential links between marine heatwave and record whale entanglements

Jarrod A. Santora, Nathan J. Mantua, Isaac D. Schroeder et al. · 2020 · Nature Communications · 255 citations

Behavioural estimation of blue whale movements in the Northeast Pacific from state-space model analysis of satellite tracks

Helen Bailey, BR Mate, Daniel M. Palacios et al. · 2009 · Endangered Species Research · 238 citations

ESR Endangered Species Research Contact the journal Facebook Twitter RSS Mailing List Subscribe to our mailing list via Mailchimp HomeLatest VolumeAbout the JournalEditorsSpecials ESR 10:93-106 (20...

Status of the world's baleen whales

Peter O. Thomas, Randall R. Reeves, Robert L. Brownell · 2015 · Marine Mammal Science · 207 citations

Abstract No global synthesis of the status of baleen whales has been published since the 2008 IUCN Red List assessments. Many populations remain at low numbers from historical commercial whaling, w...

Strong maternal fidelity and natal philopatry shape genetic structure in North Pacific humpback whales

CS Baker, Debbie Steel, John Calambokidis et al. · 2013 · Marine Ecology Progress Series · 196 citations

Reading Guide

Foundational Papers

Start with Marques et al. (2012, 697 citations) for acoustic capture methods; then Bailey et al. (2009, 238 citations) for state-space movement modeling; Reeves et al. (2012, 385 citations) contextualizes bycatch impacts.

Recent Advances

Santora et al. (2020, 255 citations) links heatwaves to entanglements; Shiu et al. (2020, 194 citations) advances neural photo-ID; Thomas et al. (2015, 207 citations) reviews baleen whale status.

Core Methods

Lincoln-Petersen extended to Jolly-Seber for open populations; Cormack-Jolly-Seber for recaptures; photo-ID with hyperdusting software; state-space for tracks; acoustic cue-counting.

How PapersFlow Helps You Research Capture-Recapture Models for Marine Populations

Discover & Search

Research Agent uses searchPapers and citationGraph to map capture-recapture literature from Marques et al. (2012), revealing 697 citations including bycatch (Reeves et al., 2012) and whale genetics (Baker et al., 2013). exaSearch finds photo-ID studies in sharks; findSimilarPapers expands to multisite models.

Analyze & Verify

Analysis Agent applies readPaperContent to extract state-space models from Bailey et al. (2009), then verifyResponse with CoVe checks emigration assumptions. runPythonAnalysis simulates tag-loss scenarios using NumPy/pandas on abundance data; GRADE assigns A-grade to Marques et al. (2012) for methodological rigor.

Synthesize & Write

Synthesis Agent detects gaps in temporary emigration handling across papers, flagging contradictions between acoustic (Marques et al., 2012) and photo-ID methods (Meekan et al., 2006). Writing Agent uses latexEditText and latexSyncCitations to draft model equations, latexCompile for PDF output, exportMermaid for movement diagrams.

Use Cases

"Simulate capture-recapture bias from tag loss in whale data."

Research Agent → searchPapers → Analysis Agent → runPythonAnalysis (pandas bootstrap resampling on Marques 2012 data) → matplotlib density plots output.

"Write LaTeX review of photo-ID abundance models for humpback whales."

Research Agent → citationGraph (Baker 2013) → Synthesis → gap detection → Writing Agent → latexEditText + latexSyncCitations + latexCompile → camera-ready PDF.

"Find code for state-space models in marine tracking papers."

Research Agent → paperExtractUrls (Bailey 2009) → Code Discovery → paperFindGithubRepo → githubRepoInspect → R/JAGS code for movement models output.

Automated Workflows

Deep Research workflow conducts systematic review: searchPapers on 'capture-recapture marine' → citationGraph → readPaperContent on top 50 → GRADE + synthesize → structured report on model evolution. DeepScan applies 7-step analysis to verify emigration bias in Bailey et al. (2009) with CoVe checkpoints. Theorizer generates hypotheses linking heatwaves to entanglement via compressed habitats (Santora et al., 2020).

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Frequently Asked Questions

What defines capture-recapture models for marine populations?

Mark-recapture and photo-ID methods estimate abundance while modeling tag loss, emigration, and movements in species like whales and sharks.

What are core methods in this subtopic?

Multi-event capture-recapture, state-space models from satellite tracks (Bailey et al., 2009), passive acoustic density estimation (Marques et al., 2012), and photo-ID mark-recapture (Meekan et al., 2006).

What are key papers?

Marques et al. (2012, 697 citations) on acoustics; Reeves et al. (2012, 385 citations) on bycatch; Baker et al. (2013, 196 citations) on humpback photo-ID structure.

What open problems exist?

Integrating real-time satellite tagging with photo-ID for dynamic populations; scaling deep neural detection (Shiu et al., 2020) to low-data species; modeling climate impacts on movements (Grémillet and Boulinier, 2009).

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Part of the Marine animal studies overview Research Guide