Peer Review #2 of "A simulation-based evaluation of methods for estimating census population size of terrestrial game species from genetically-identified parent-offspring pairs (v0.1)" DOI Creative Commons
Jérémy Larroque, Niko Balkenhol

Published: April 12, 2023

Estimates of wildlife population size are critical for conservation and management, but accurate estimates difficult to obtain many species.Several methods have recently been developed that estimate abundance using kinship relationships observed in genetic samples , particularly parent-offspring pairs .While these similar traditional Capture-Mark-Recapture, they do not need physical recapture, as individuals considered recaptured if a sample contains one or more close relatives.This makes based on genetically-identified interesting species which releasing marked animals back into the is desirable possible (e.g., harvested fish game species).However, while successfully applied commercially important species, absence lifehistory data, making several assumptions unlikely be met terrestrial species.They assume only generation parents juveniles year, than two generations can coexist hunting bags long-lived sampling probability same each individual, an assumption violated when fecundity and/or survival depend sex other individual traits.In order assess usefulness kin-based sizes we simulated pedigrees different with contrasting demographic strategies (wild boar red deer), four compared accuracy precision their estimates.We also performed sensitivity analysis, simulating varying characteristics various levels harvesting identify optimal conditions applicability method.We showed all reached required effective management under circumstances (i.e., within given range intensity), being robust variation.Despite potential care needed

Language: Английский

Comparison of kinship‐identification methods for robust stock assessment using close‐kin mark–recapture data for Pacific bluefin tuna DOI Creative Commons
Yohei Tsukahara, Reiichiro Nakamichi,

Aiko Matsuura

et al.

Population Ecology, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 2, 2025

Abstract Several attempts have been made to understand the population dynamics of fishery resources, such as tuna species using an integrated analysis model with multiple data sources. However, estimating absolute abundance levels in practical stock assessments remains a challenge. Close‐kin mark–recapture (CKMR) methods provide information about number adults close‐kinship pairs identified by genetic markers and statistical methods. In this study, we compared three for kinship identification different algorithms samples wild Pacific bluefin genotyped across 5029 genome‐wide single nucleotide polymorphisms 4108 samples. The flexible relationship analyzer random forest method developed employs pairwise identity‐by‐descent values inputs classification. other two were CKMRsim COLONY, which published applied several studies. These actual genotyping moderate missing genotypes, addition pseudo‐generated simulation test. test mimicked physical linkages well characteristics similar those resulted numbers inferred both generated data. Particularly half‐sibling pairs, considerable false‐positives false‐negatives existed results. differences results interpreted based on This study may enhance understanding how each software performs when single‐nucleotide polymorphism demonstrated study.

Language: Английский

Citations

1
Key role of fisheries genomics to support conservation, fisheries management and trade of widely-distributed spiny lobsters DOI Creative Commons
Éva E. Plagányi, Laura K. Blamey, Roy A. Deng

et al.

Fisheries Research, Journal Year: 2025, Volume and Issue: 281, P. 107266 - 107266

Published: Jan. 1, 2025

Language: Английский

Citations

1
Accounting for unobserved population dynamics and aging error in close‐kin mark‐recapture assessments DOI Creative Commons
John D. Swenson, Elizabeth N. Brooks, Dovi Kacev

et al.

Ecology and Evolution, Journal Year: 2024, Volume and Issue: 14(2)

Published: Feb. 1, 2024

Abstract Obtaining robust estimates of population abundance is a central challenge hindering the conservation and management many threatened exploited species. Close‐kin mark‐recapture (CKMR) genetics‐based approach that has strong potential to improve monitoring data‐limited species by enabling abundance, survival, other parameters for populations are challenging assess. However, CKMR models have received limited sensitivity testing under realistic dynamics sampling scenarios, impeding application method in programs stock assessments. Here, we use individual‐based simulation examine how unmodeled aging uncertainty affect accuracy precision parameter different strategies. We then present adapted correct biases arise from model misspecification. Our results demonstrate simple base‐case produces with stable breed annually; however, if trend or non‐annual breeding present, year‐specific desired, more complex must be constructed. In addition, show can generate reliable adults variety strategies, including juvenile‐focused where never directly observed (and error minimal). Finally, apply been growth intermittent two decades genetic data juvenile lemon sharks ( Negaprion brevirostris ) Bimini, Bahamas, samples drawn solely juveniles contribute efforts highly mobile populations. Overall, this study expands our understanding biological factors decisions cause bias models, identifies key areas future inquiry, provides recommendations aid biologists planning implementing an effective study, particularly long‐lived

Language: Английский

Citations

8
How Can Genomics Help or Hinder Wildlife Conservation? DOI Creative Commons
Thomas L. Schmidt, Joshua A. Thia, Ary A. Hoffmann

et al.

Annual Review of Animal Biosciences, Journal Year: 2023, Volume and Issue: 12(1), P. 45 - 68

Published: Oct. 3, 2023

Genomic data are becoming increasingly affordable and easy to collect, new tools for their analysis appearing rapidly. Conservation biologists interested in using this information assist management planning but typically limited financially by the lack of genomic resources available non-model taxa. It is therefore important be aware pitfalls as well benefits applying approaches. Here, we highlight recent methods aimed at standardizing population assessments genetic variation, inbreeding, forms load that help identify past ongoing patterns interchange between populations, including those subjected disturbance. We emphasize challenges some these need adequate bioinformatic support. also consider promises approaches understand adaptive changes natural populations predict future capacity.

Language: Английский

Citations

14
Sources of bias in applying close‐kin mark–recapture to terrestrial game species with different life histories DOI Creative Commons
Anthony Sévêque, Robert C. Lonsinger, Lisette P. Waits

et al.

Ecology, Journal Year: 2024, Volume and Issue: 105(3)

Published: Jan. 25, 2024

Abstract Close‐kin mark–recapture (CKMR) is a method analogous to traditional but without requiring recapture of individuals. Instead, multilocus genotypes (genetic marks) are used identify related individuals in one or more sampling occasions, which enables the opportunistic use samples from harvested wildlife. To apply accurately, it important build appropriate CKMR models that do not violate assumptions linked species’ and population's biology methods. In this study, we evaluated implications fitting overly simplistic populations with complex reproductive success dynamics selective sampling. We forward‐in‐time, individual‐based simulations evaluate accuracy precision abundance survival estimates species different longevities, mating systems, strategies. Simulated approximated range life histories among game North America lethal potential using estimate population size. Our show can yield nontrivial biases both estimates, unless influential history traits explicitly accounted for modeling framework. The number kin pairs observed sample, combination type kinship model (parent–offspring and/or half‐sibling pairs), affect estimates. promising will likely see an increasing applications field as costs genetic analysis continue decline. work highlights importance applying population‐specific consider relevant demographic parameters, individual covariates, protocol through were sampled.

Language: Английский

Citations

5
Spatial close‐kin mark‐recapture models applied to terrestrial species with continuous natal dispersal DOI Creative Commons
Anthony Sévêque, Robert C. Lonsinger, Lisette P. Waits

et al.

Methods in Ecology and Evolution, Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 13, 2025

Abstract Close‐kin mark–recapture (CKMR) methods use information on genetic relatedness among individuals to estimate demographic parameters. An individual's genotype can be considered a ‘recapture’ of each its parent's genotype, and the frequency kin‐pair matches detected in population sample directly inform estimates abundance. CKMR inference procedures require analysts define kinship probabilities functional forms, which inevitably involve simplifying assumptions. Among others, structure have strong influence how are formulated. Many terrestrial species philopatric or face barriers dispersal, not accounting for dispersal limitation probabilities, create substantial bias if sampling is also spatially structured (e.g. via harvest). We present explicit formulation that corrects incomplete mixing by incorporating natal distances spatial distribution into probabilities. used individual‐based simulations evaluate accuracy abundance obtained with one naïve two models across six scenarios distinct patterns relative probability. Estimates model were negatively biased when was biased. Incorporating helped address this bias, but always accurate depending scenario considered. created heterogeneous will often additional assumptions auxiliary data indices). The shown here designed continuous high year‐to‐year site fidelity could extended other species.

Language: Английский

Citations

0
Close-Kin Mark-Recapture Without Age Information: Application to Southern Right Whales DOI Creative Commons
Brage Førland, Hans J. Skaug, Megumi Takahashi

et al.

Journal of Agricultural Biological and Environmental Statistics, Journal Year: 2025, Volume and Issue: unknown

Published: April 24, 2025

Language: Английский

Citations

0
Close-kin mark-recapture informs critically endangered terrestrial mammal status DOI Creative Commons
Luke R. Lloyd‐Jones, Mark V. Bravington, Kyle N. Armstrong

et al.

Scientific Reports, Journal Year: 2023, Volume and Issue: 13(1)

Published: Aug. 2, 2023

Abstract Reliable information on population size is fundamental to the management of threatened species. For wild species, mark-recapture methods are a cornerstone abundance estimation. Here, we show first application close-kin (CKMR) method terrestrial species high conservation value; Christmas Island flying-fox (CIFF). The CIFF island's last remaining native mammal and was recently listed as critically endangered. CKMR powerful tool for estimating demographic parameters central circumvents complications arising from species’ cryptic nature, mobility, difficult-to-survey habitat. To this end, used genetic data 450 CIFFs captured between 2015 2019 detect kin pairs. We implemented novel model that estimates sex-specific abundance, trend, mortality accommodates observations kin-pair distribution male reproductive skew mate persistence. estimated total adult female be approximately 2050 individuals (95% CI (950, 4300)). showed average only 23% contributed annual reproduction strong evidence between-year fidelity, an observation not previously quantified Pteropus in wild. Critically, our provide most robust understanding status endangered population, informing immediate future initiatives.

Language: Английский

Citations

9
Reliability of trans‐generational genetic mark–recapture (tGMR) for enumerating Pacific salmon DOI Creative Commons
Samuel W. Rosenbaum, Samuel A. May, Kyle R. Shedd

et al.

Evolutionary Applications, Journal Year: 2024, Volume and Issue: 17(2)

Published: Feb. 1, 2024

As Pacific salmon (

Language: Английский

Citations

3
Estimating effective population size using close‐kin mark–recapture DOI Creative Commons
Jonathan Babyn, Daniel E. Ruzzante, Mark V. Bravington

et al.

Methods in Ecology and Evolution, Journal Year: 2024, Volume and Issue: unknown

Published: Sept. 18, 2024

Abstract Close‐kin mark–recapture (CKMR) is a method that allows estimating population census size, among other parameters, through the observed number of pairs are close‐kin including parent–offspring (POPs) and half‐sibling (HSPs). CKMR models capable abundance, fecundity survival at age using POPs HSPs from different cohorts. The link between effective size ( N e ) ‘within‐cohort’ sibling has been noted before but how to actually achieve such an estimate with not previously demonstrated. We show it possible use along ‘different‐cohort’ . These can be combined annual variance in offspring lifetime total reproductive success which used find produced by adults given year related within‐cohort comparisons. Our approach demonstrated on individual‐based simulation where we offers similar results estimated methods like linkage disequilibrium. allow while also demographic parameters.

Language: Английский

Citations

2