Mark Loss Research Articles

Theory of epigenetic switching due to stochastic histone mark loss during DNA replication

How much information does a cell inherit from its ancestors beyond its genetic sequence? What are the epigenetic mechanisms that allow this? Despite the rise in available epigenetic data, how such information is inherited through the cell cycle is still not fully understood. Often, epigenetic marks can display bistable behaviour and their bistable state is transmitted to daughter cells through the cell cycle, providing the cell with a form of memory. However, loss-of-memory events also take place, where a daughter cell switches epigenetic state (with respect to the mother cell). Here, we develop a framework to compute these epigenetic switching rates, for the case when they are driven by DNA replication, i.e. the frequency of loss-of-memory events due to replication. We consider the dynamics of histone modifications during the cell cycle deterministically, except at DNA replication, where nucleosomes are randomly distributed between the two daughter DNA strands, which is therefore implemented stochastically. This hybrid stochastic-deterministic approach enables an analytic derivation of the replication-driven switching rate. While retaining great simplicity, this framework can explain experimental switching rate data, establishing its biological importance as a framework to quantitatively study epigenetic inheritance.

Public perception of the Sumatran elephant conflict in the village buffer region GLNP and economic loss consequence of the conflict

The Sumatran Elephant (Elephas maximus sumatranus) is registered with IUCN Red List with status threatened extinct (endangered species). Conflict that occurs between humans and elephants is increasing from time to time. Change of forest land to agricultural land and settlements are the main causes of the occurrence conflict. This study aims to determine community perceptions, the effectiveness of mitigation and the value of losses economic response to the Sumatran elephant conflict. The method used in this study is by observation and interview through charging questionnaire to selected respondents. Respondents determined in a manner random from population at the estimated location as a distribution area elephant in the village GLNP Area Buffer Location studies shared into 24 grids, with wide each grid is 5x5 km. In each grid determined 3 respondents. Results study show 20% respondent experience conflict and 80% respondent No caught conflict. Mitigation conflict For drive away elephants considered the most effective by the community is with cannon spirit. Amount loss public in 3 year final reach IDR 58,000,000.00. Mark loss smallest i.e. as big Rp 500,000.00 on lemongrass.

Audiovisual artefacts: the African politics of moving image loss

ABSTRACT Artefacts are human-made objects deemed culturally and historically significant. But they are also those scratches, burns and glitches that appear on audiovisual screens due to poor projection, improper storage or faulty processing. They are those unwanted additions that visualise the presence of loss. This paper explores the politics of audiovisual loss by looking at the history of the Ghana Film Industry Corporation film collection’s demise alongside the 2020 films by Onyeka Igwe – a so-called archive and No Archive Can Restore You – that feature a similar collection in Nigeria. Igwe’s exploratory camera floats around the Nigerian Film Corporation building documenting the filmic carnage within its vaults, reminding audiences that archival horror lies in the “colonial residue” of the archive’s architecture. Artefacts of decay in Igwe’s films, that mark the elimination of information from the image that restoration seeks to renew, are not the result of inaction, but acts of refusal. Film artefacts not only mark loss but are also traces of postcolonial affect. As such, I argue that archival neglect and the losses that it produces may also be acts of archival labour – an articulation of artefacting.

Mark loss can strongly bias estimates of demographic rates in multi-state models: a case study with simulated and empirical datasets

Mark loss can strongly bias estimates of demographic rates in multi-state models: a case study with simulated and empirical datasets

MBD4 loss results in global reactivation of promoters and retroelements with low methylated CpG density

BackgroundInherited defects in the base-excision repair gene MBD4 predispose individuals to adenomatous polyposis and colorectal cancer, which is characterized by an accumulation of C > T transitions resulting from spontaneous deamination of 5’-methylcytosine.MethodsHere, we have investigated the potential role of MBD4 in regulating DNA methylation levels using genome-wide transcriptome and methylome analyses. Additionally, we have elucidated its function through a series of in vitro experiments.ResultsHere we show that the protein MBD4 is required for DNA methylation maintenance and G/T mismatch repair. Transcriptome and methylome analyses reveal a genome-wide hypomethylation of promoters, gene bodies and repetitive elements in the absence of MBD4 in vivo. Methylation mark loss is accompanied by a broad transcriptional derepression phenotype affecting promoters and retroelements with low methylated CpG density. MBD4 in vivo forms a complex with the mismatch repair proteins (MMR), which exhibits high bi-functional glycosylase/AP-lyase endonuclease specific activity towards methylated DNA substrates containing a G/T mismatch. Experiments using recombinant proteins reveal that the association of MBD4 with the MMR protein MLH1 is required for this activity.ConclusionsOur data identify MBD4 as an enzyme specifically designed to repair deaminated 5-methylcytosines and underscores its critical role in safeguarding against methylation damage. Furthermore, it illustrates how MBD4 functions in normal and pathological conditions.

Neckband loss and its effect on apparent survival estimates in Greylag Geese (Anser anser): variation with season, sex and age

Mark-recapture studies enable us to estimate population parameters such as survival, if marks do not impact survival and if marks are not lost. Mark loss can result from external wear and damage, but also behavioural factors may be important and could explain differences between seasons or sexes. We studied Greylag Geese (Anser anser) in eastern Netherlands, ringed with neckbands, leg bands and metal rings (912 geese), observed weekly during 1997–2019 (131,625 observations). Given the double marking and high annual resighting probabilities (neckbands: 0.974, leg rings: 0.639), we quantified neckband loss and the effect of neckbands on apparent survival, using multistate mark-recapture models. Annual neckband loss was 0.038, was higher in males (0.056) than females (0.021) and increased with years since marking, up to 0.098 for males more than 8 years after marking. Neckband loss tended to be higher during December–May than June–November, with most losses occurring in March–April. Both the higher loss in males and the peak in spring in both sexes could result from intraspecific fighting (pulling each other’s neck and neckband). Survival was underestimated in Cormack-Jolly-Seber models that did not account for neckband loss, by up to 0.096 for adult males 6–7 years after marking. Thus, ignoring neckband loss may give erroneous survival differences between sexes and seasons, and overestimate the effect of ageing on survival (i.e. senescence). We did not detect an effect of neckbands on mortality, but statistical power for this test was limited. Neckband loss, although lower nowadays than in studies of decades ago, still impacts survival estimates and should be considered in mark-recapture studies.

Survival and breeding interval of an endangered marine vertebrate, the leatherback turtle Dermochelys coriacea, in French Guiana

In the context of global change, endangered species such as sea turtles undergo strong population dynamics changes. Understanding demographic processes inducing such changes is critical for developing appropriate measures for conservation and management. Nesting females of the French Guiana population of leatherback sea turtles Dermochelys coriacea represented 40% of the world’s total in 2001; today, they represent only 10%. Here, we analyze data from the long-term monitoring program of leatherbacks in French Guiana, based on 28 yr of capture-mark-recapture data from 46051 individuals in northwestern French Guiana. We used multievent models (multistate capture-recapture models with state uncertainty) to represent the main peculiarity of the life cycle, intermittent reproduction, and to take advantage of the use of several different types of marks to account for mark loss and incomplete detection. The average annual adult survival probability (mean ± SE) 0.789 ± 0.009 is low compared to published estimates for this species. By combining the estimates of departure and return probabilities, we provide an estimate of the interval among laying seasons equal to 2.777 ± 0.118 yr, which matches previous findings. Taking survival into account, this interval translates into an average of 1.704 ± 0.034 further reproductive seasons for an adult female having just bred, which is remarkably low compared to other long-lived vertebrates. The representation of the life cycle and mark loss in our models provides a sound structure for broader and richer analyses to extract biological information from marked individuals and offers an invaluable source of demographic information on leatherbacks, a species for which only a small segment of the population is accessible to intermittent sampling.

Use of photography to identify free-roaming dogs during sight-resight surveys: Impacts on estimates of population size and vaccination coverage, Haiti 2016

BackgroundEnumerating dog populations is essential to plan and evaluate rabies vaccination campaigns. To estimate vaccination coverage and dog population size in a Haitian commune, 15 sight-resight counts were conducted over two days following a government-sponsored vaccination campaign. MethodsDogs received temporary laminated collars and livestock wax marks on the head and sides at the time of rabies vaccination. After the vaccination campaign, pairs of surveyors walked pre-defined routes through targeted neighborhoods, photographing and recording characteristics and location of each dog seen on a standardized data sheet. On the second survey day, surveyors retraced the prior day’s track, followed the same procedure, and indicated in addition whether they believed the dogs were resighted from the prior day. After completion of the field survey, two independent evaluators reviewed photographs and characteristics of each dog to assess which had vaccination marks and which were resighted. Surveyor and photo-reviewer sight-resight decisions were compared using Cohen’s kappa, and population estimates were compared using Lincoln-Petersen 95% confidence intervals. ResultsField-surveyors identified dogs consistent with the photograph evaluations in 629 out of 800 instances (78.6%, Cohen’s kappa of 0.12). Despite this inconsistency, the population estimates resulting from the field and final determinations were not significantly different at 1,789 (95% CI 1,677 to 1,901) and 1,978 (95% CI 1,839 to 2,118). Vaccination coverage was also the same at 55% and 56%; however, an observed vaccination mark loss of 13.8% suggests that the true coverage may have been closer to 64%. ConclusionUsing photos improved dog identification during the sight-resight study, leading to a higher population estimate. Despite using a 2-mark system to temporarily identify vaccinated dogs, a significant proportion had lost all identifying marks by the second day of field surveys. Efforts to estimate vaccination coverage using sight-resight surveys should consider improvement of marking techniques or better accounting for potential loss of marks in their free-roaming dog vaccination coverage assessments.

A model for first‐estimates of species‐specific, age‐specific mortality from centralized band‐recovery databases

AbstractPopulation mortality curves, otherwise known as lifetime distribution functions, can be indispensable in many areas of ecology and environmental management including population viability and stock management analyses, disaster‐recovery monitoring, and fundamental evolutionary biology. Yet available modeling tools are often unable to estimate population mortality curves from commonly available datasets because these datasets fail to meet stringent experimental‐design requirements. Here, we present a new method for estimating population mortality curves from records of marked individuals found dead. Such data are increasingly accessible in some of the largest biological datasets, such as continent‐ or nation‐wide marking‐and‐recovery schemes for birds and other animals. The method accounts for known biases in availability by age class, variable monitoring effort through time, and mark loss. We show that our modeling approach generates accurate estimates of population mortality structure across a range of populations differing in marking histories, true mortality curves, monitoring regimes, and mark loss rates. Our approach can be applied to multiple species or groups at a time and can provide estimates of inter‐annual adult, immature, and first‐year survival rates, required by predictive modeling applications such as population viability analyses. Our approach is also capable of estimating apparent senescence rates for each population and facilitates evolutionary analyses of life‐history traits. For example, our method is potentially useful for exploring the evolution of senescence or for inter‐group comparisons of mortality rates where groups that differ by environment may be identified within mark‐recovery records. To demonstrate the efficacy of this method, we present fitted population mortality curves for a suite of seabird species represented in a national mark–recapture database.

Effects of passive integrated transponder (PIT) implantation on Pacific lamprey ammocoetes

BackgroundLittle is known of the larval biology of Pacific lamprey (Entosphenus tridentatus), a species of conservation concern. With miniaturization of passive integrated transponder (PIT) tags, researchers now have the potential to individually mark larval lamprey. However, recent studies with sea lamprey (Petromyzon marinus) ammocoetes indicated that mortality was unacceptably high after surgical implantation of these tags. We examined survival, tag retention, growth, and swimming performance of Pacific lamprey ammocoetes tagged with uniquely coded 8.4-mm PIT tags and controls marked with visible implant elastomer (VIE).ResultsAmmocoetes as small as 71 mm in length were PIT-tagged. Of the 99 PIT-tagged individuals, four died (4%) and two lost their tags (2%) within 2 months of tagging. In this period, controls had 5% mortality and 15% VIE mark loss. Incisions were completely healed within 3 months of tagging, and mean specific growth rate during this period did not significantly differ between treatment groups. Ammocoetes bearing a PIT tag did not exhibit significant reductions in swimming performance relative to controls.ConclusionsWe attribute the success of this tagging effort to changes in tag implantation technique, including use of a lateral incision and no sutures. The ability to individually mark wild larval lamprey will allow research on individual growth rates, environmental effects on growth and metamorphosis, timing and rates of movement, and, ultimately, stage-specific survival.

Measuring neck collar loss of Pink-footed Geese Anser brachyrhynchus

Capsule The ability to estimate mark loss of ringed animals is important to assess demographic parameters from mark-recapture studies correctly. Based on 23 years of neck collar recovery data from the Svalbard breeding population of Pink-footed Geese, we estimate an overall average annual loss rate of 3.2%. Neck collar loss was similar between males and females, and did not (based on currently available data) differ significantly between two types of collars used.

Hidden Markov Model for Dependent Mark Loss and Survival Estimation

Mark-recapture estimators assume no loss of marks to provide unbiased estimates of population parameters. We describe a hidden Markov model (HMM) framework that integrates a mark loss model with a Cormack–Jolly–Seber model for survival estimation. Mark loss can be estimated with single-marked animals as long as a sub-sample of animals has a permanent mark. Double-marking provides an estimate of mark loss assuming independence but dependence can be modeled with a permanently marked sub-sample. We use a log-linear approach to include covariates for mark loss and dependence which is more flexible than existing published methods for integrated models. The HMM approach is demonstrated with a dataset of black bears (Ursus americanus) with two ear tags and a subset of which were permanently marked with tattoos. The data were analyzed with and without the tattoo. Dropping the tattoos resulted in estimates of survival that were reduced by 0.005–0.035 due to tag loss dependence that could not be modeled. We also analyzed the data with and without the tattoo using a single tag. By not using. Supplementary materials accompanying this paper appear on-line.

Photo-identification and the effects of tagging on the Patagonian catfish Hatcheria macraei

Effects of subcutaneous visible implanted alphanumeric (VIA) microtags, pelvic fin excision, and individual photo-identification (Pid) based on natural spot patterns were experimentally evaluated in the small stream benthic Patagonian catfish Hatcheria macraei. VIA tag retention was 90 % during the first 45 days, decreasing to 80 % at day 200, and 66 % at the end of the experiment, at day 254. Fin regeneration was not evident during the experiment. Survival, growth rate or condition factor (Fulton’s K) did not differ between tagged or pelvic fin clipped catfish and a control group. Spot patterns varied greatly among individuals and remained constant throughout the experimental period, thereby making identification of individual Pid possible in H. macraei. Tagging was not effective in identifying individual fish due to mark loss or difficulty in reading VIA tag codes. The combination of Pid with VIA tagging or fin clipping techniques in longterm experiments is advisable in order to facilitate individual recognition. The Pid analysis described in this study is a low-cost method that could potentially be applied to any fish with a variable spot pattern.

Factors Influencing Survival and Mark Retention in Postmetamorphic Boreal Chorus Frogs

result little is known about this life-history phase for most amphibians. Our focus was to explore survival probabilities, mark retention, and mark migration in postmetamorphic Boreal Chorus Frogs (Psuedacris maculata) in a laboratory setting. One hundred forty-seven individuals were assigned randomly to two treatment groups or a control group. Frogs in the first treatment group were marked with visual implant elastomer, while frogs in the second treatment group were toe clipped. Growth and mortality were recorded for one year and resulting data were analyzed using known-fate models in Program MARK. Model selection results suggested that survival probabilities of frogs varied with time and showed some variation among marking treatments. We found that frogs with multiple toes clipped on the same foot had lower survival probabilities than individuals in other treatments, but individuals can be marked by clipping a single toe on two different feet without any mark loss or negative survival effects. Individuals treated with visual implant elastomer had a mark migration rate of 4% and mark loss rate of 6%, and also showed very little negative survival impacts relative to control individuals.

The implications of assuming independent tag loss in southern elephant seals

Survival and reproductive rate estimation requires following uniquely identified individuals through time, and many statistical models assume markings used to identify individuals are permanent. However, survival rates are underestimated when single marks are lost, since the models will effectively score those animals as dead. In order to account for mark loss, some researchers use a double‐mark approach, assuming the probability of losing one mark is independent of losing the other one. Therefore, mark loss can be estimated using animals that have lost one mark. Using a 17‐year dataset of southern elephant seals (Mirounga leonina) marked with permanent brands and two cattle tags in their hind flippers, we were able to compare tag loss and survival rate estimates with and without the assumption of independent tag loss with respect to age, sex, and wean mass. We demonstrate the assumption of independent tag loss is not valid, showing it is more likely for an animal to lose both tags than just one or the other. The assumption of independent tag loss leads to an underestimate of survival rates which in turn leads to underestimates of population growth rate. In addition, tag loss rates are different by sex and age, with older males more likely to lose tags. Tag loss is also a quadratic function of wean mass through age two, with smaller and larger animals more likely to lose both tags. Such differences are possibly due to differences in behavior, flipper growth, and immune response. Using a Bayesian approach, we will be able to use our tag loss estimates as priors in future analyses for a subset of marked animals that only have flipper tags. With this population, the independent tag loss models are more likely to incorrectly estimate a declining population (growth rate < 1.0), potentially leading to unwarranted management action. To account for non‐independent mark loss in survival rate studies, we recommend researchers use at least two forms of marking on at least a subset of animals. However, neither form of marking need be permanent as long as mark loss is independent between the different forms.

Integrating heterogeneity of detection and mark loss to estimate survival and transience in UK grey seal colonies

Summary 1. We present new developments in statistical methodology allowing in‐depth analysis of realistic, complex biological models for longitudinal data sets. Important biological details such as mark‐loss and recapture heterogeneity can be identified. 2. We use a Bayesian hidden process framework for a comparative analysis of long‐term (1978–2006) capture–recapture data with various combinations of marking methods for adult female grey seals Halichoerus grypus at two UK colonies. 3. Seals were identified using three different methods: flipper tags, brands, or natural pelage markings. Animals identified by brands or natural markings were re‐sighted more effectively than those with tags. 4. Flipper tag‐loss rates differed between colonies, and there was evidence for non‐independent tag‐loss in double‐tagged animals. There was also evidence at one colony for the presence of transient animals, which attend the colony for 1 year only. Apparent survival was higher and more consistent at one site, and the differences in survival between the two colonies were able to explain contrasting pup production trends at these sites. 5. Synthesis and applications. Longitudinal studies allow for the estimation of demographic parameters which have important implications for our understanding of population dynamics and for the conservation and management of populations. Using new statistical developments to allow for the analysis of missing/incomplete data and partial observations, we show how survival can be estimated from complex mark–recapture data, allowing for the effects of mark loss. The re‐sightability of different marks is estimated, indicating that photo‐ID based on natural pelage markings is a very effective method for identifying grey seals. There are notable contrasts in survival estimates between breeding colonies which can explain contrasts in population trends at these sites, confirming the importance of adult survival in driving population dynamics in this long‐lived species.

A Capture–Recapture Model with Double-Marking, Live and Dead Encounters, and Heterogeneity of Reporting Due to Auxiliary Mark Loss

Capture–recapture (CR) models assume marked individuals remain at risk of capture, which may not be true if individuals lose their mark or emigrate definitively from the study area. Using a double-marking protocol, with a main and auxiliary mark, and both live encounters and dead recoveries at a large scale, partially frees CR models from this assumption. However, the auxiliary mark may fall off and its presence is often not mentioned when dead individuals are reported. We propose a new model to deal with heterogeneity of detection and uncertainty of the presence of an auxiliary mark in a multi-event framework. Our general model, based on a double-marking protocol, uses information from physical captures/recaptures, distant observations and main mark recoveries from dead animals. We applied our model to a 13-year data set of a harvested species, the Greater Snow Goose. We obtained seasonal survival estimates for adults of both sexes. Survival estimates differed between models where the presence of the auxiliary mark upon recovery was ignored versus those where the presence was accounted for. In the multi-event framework, seasonal survival estimates are no longer biased because the heterogeneity due to the presence of an auxiliary mark is accounted for in the estimation of recovery rates.

Integrated data analysis in the presence of emigration and mark loss

Integrated data analyses are becoming increasingly common in studies of wild animal populations where two or more separate sources of data contain information about common parameters. These types of analyses provide robust parameter estimates which fully reflect all available information, as well as estimates of parameters that would be unidentifiable in a separate analysis. In this article we present an integrated Bayesian analysis of four long-term datasets (counts, two mark-recapture-recovery time series, and productivity) relating to a colony of common guillemots (Uria aalge) on the Isle of May, southeast Scotland. A complication when considering the dynamics of populations of this kind is the unobservable emigration of immature animals. In the analysis of mark-recapture-recovery data, the rate of emigration is frequently confounded with that of mark loss and it is only possible to estimate the product of these parameters. By combining all available data for the Isle of May guillemots in an integrated population model, we are able to estimate these parameters separately and thus obtain improved estimates of prerecruitment emigration.

Tag loss probabilities are not independent: Assessing and quantifying the assumption of independent tag transition probabilities from direct observations

The ability to identify animals individually throughout their lives is a cornerstone of sound population ecology research. However, because not all marks are permanent it is important to accurately account for the loss of marks. To this end, animals are often marked with two marks to limit the chance of the animal being presumed dead i.e. lost to the study by being individually unidentifiable, when actually alive. To account for the eventuality that both marks are lost, mark loss rates are generally assumed to be independent and adjustments to the number of animals alive are made accordingly. This assumption that tags on the same animal are lost independently was tested within the multi-model-inference framework in a study of 5928 branded, tagged and weighed (at weaning) elephant seals at Macquarie Island. Our key finding was that the probability of loosing a second tag after the first had been lost was dependent on the probability of having already lost a first tag and that on average there was a 28.1% greater likelihood of loosing a second tag once the first had been lost. Indeed, there was no support (ΔQAIC c > 64.5) for models which included this assumption of independence. We found little evidence for differences in the tag loss rates between the sexes (ER = 1.08, i.e. models with and without the gender/sex variable were equivalent). However, we did find that heavier seals were more likely to retain their tags ( ψ 2:2 and ψ 1:1 combined) than lighter seals (0.96 year − 1 and 0.83 year − 1 respectively), and that lighter seals were more likely to move into the zero tag state than heavier seals ( ψ 2:0 0.386 year − 1 and 0.187 year − 1 respectively and ψ 1:0 0.121 year − 1 and 0.057 year − 1 respectively). We suggest that tag loss in lighter seals may exhibit a higher degree of dependence than heavier seals. Using age and site specific tag loss estimates are crucial when correcting survival estimates in mark–-recapture studies because there are a number of factors that may be responsible for differences in the rates of loss e.g. tag placement and animal condition. Importantly, there is a growing body of evidence, to which this study contributes, showing that the general assumption of independence to calculate double tag loss is flawed, we suggest that where possible permanent methods of marking should be considered ahead of other non-permanent methods.

Surface damage analysis of retrieved highly crosslinked polyethylene tibial components after short‐term implantation

The use of highly crosslinked polyethylene (PE) in the knee remains controversial, because of reduced fatigue fracture properties of the material. The current study investigated postmelt surface damage as well as potential contributors to this damage in retrieved highly crosslinked PE tibial components, after short-term in vivo durations. Retrieved conventional PE tibial components were examined for comparison, as well as unused time zero highly crosslinked and conventional PE tibial components for inherent manufacturing surface characterization. Predominant surface damage modes on highly crosslinked PE components were machine mark loss and abrasion, while conventional PE components primarily had machine mark loss, abrasion, and delamination. In vivo duration, PE thickness, and conformity of the design were significant predictors of surface damage on retrieved conventional PE components. Donor weight and the conformity of the design were significant predictors of surface damage on retrieved highly crosslinked PE components. This retrieval data on highly crosslinked PE tibial components suggest that in vivo wear occurred, observed as postmelt surface damage. The highly crosslinked Durasul material examined in this retrieval study appeared to outperform the conventional PE components made from 4150 resin, ram-extruded and gamma-sterilized in air, but not the conventional components made from 1020 resin, compression molding and gamma sterilization in nitrogen. Early retrieval data of highly crosslinked PE tibial components are important to serve as a benchmark to be compared with future longer-term retrieval studies investigating whether surface damage translates to clinically relevant particulate wear debris generation and PE clinical performance.