Metapopulation Structure Research Articles

Evidence for metapopulation structure in seep-dwelling amphipods

Twelve seepage springs in a 3 km2 area of the Goldmine Tract in the C&O Canal National Historical Park in Montgomery County, Maryland, USA were sampled in 1994–1995 and again in 2023 for three amphipod species: Stygobromus tenuis potomacus, Stygobromus pizzinii, and Crangonyx shoemakeri. During that time interval, there were 11 colonizations and 1 exinction. Three populations persisted. These results are consistent with the proposed metapopulation hypothesis of population structure.

New survey data on abundance and movements for two poorly known Asian Spiny Frogs

We present new natural history data on abundance and movements (daily and seasonal) during the pre-breeding (March-June) and breeding-post-breeding season (July-September) of two poorly studied frog species of the Himalayas, Nanorana vicina and Allopaa hazarensis. We estimated 185 Murree Hills Frogs and 90 Hazara Frogs within the study area (0.79 ha). The daily and seasonal movement data showed that the two species moved either between neighboring ponds or remained in an array of smaller ponds (within an area of 120 m2) along the stream bank. About 75% of movements were < 29.5 m in N. vicina and < 50.87 m in A. hazarensis during pre-breeding season while < 41.5 m in N. vicina and < 81 m in A. hazarensis during breeding-post-breeding season. We suggest inclusion of amphibian habitat requirements and ensuring stream connectivity in urban planning and development projects in the area to prevent the local extinction of the endemic species. In the future, more robust and long-term studies, encompassing more streams situated within a wider area, would help clarify dispersal, colonization, metapopulation structure, and dynamics of these endemic frogs of the forested montane streams in the Himalayan Foothills.

The role of the ecological scaffold in the origin and maintenance of whole-group trait altruism in microbial populations

BackgroundKin and multilevel selection provide explanations for the existence of altruism based on traits or processes that enhance the inclusive fitness of an altruist individual. Kin selection is often based on individual-level traits, such as the ability to recognize other altruists, whereas multilevel selection requires a metapopulation structure and dispersal process. These theories are unified by the general principle that altruism can be fixed by positive selection provided the benefit of altruism is preferentially conferred to other altruists. Here we take a different explanatory approach based on the recently proposed concept of an “ecological scaffold”. We demonstrate that ecological conditions consisting of a patchy nutrient supply that generates a metapopulation structure, episodic mixing of groups, and severe nutrient limitation, can support or “scaffold” the evolution of altruism in a population of microbes by amplifying drift. This contrasts with recent papers in which the ecological scaffold was shown to support selective processes and demonstrates the power of scaffolding even in the absence of selection.ResultsUsing computer simulations motivated by a simple theoretical model, we show that, although an altruistic mutant can be fixed within a single population of non-altruists by drift when nutrients are severely limited, the resulting altruistic population remains vulnerable to non-altruistic mutants. We then show how the imposition of the “ecological scaffold” onto a population of non-altruists alters the balance between selection and drift in a way that supports the fixation and subsequent persistence of altruism despite the possibility of invasion by non-altruists.ConclusionsThe fixation of an altruistic mutant by drift is possible when supported by ecological conditions that impose a metapopulation structure, episodic mixing of groups, and severe nutrient limitation. This is significant because it offers an alternative explanation for the evolution of altruism based on drift rather than selection. Given the ubiquity of low-nutrient “oligotrophic” environments in which microbes exist (e.g., the open ocean, deep subsurface soils, or under the polar ice caps) our results suggest that altruistic and cooperative behaviors may be highly prevalent among microbial populations.

Severe, large-scale bushfire threatens metapopulation function of quokka (Setonix brachyurus) in south-western Australia

Background The risk of large, severe bushfires is increasing in Australia, and little is known about their impact on threatened species. Aims This study aimed to investigated the abundance, occupancy and metapopulation structure of the quokka (Setonix brachyurus) for 5 years following a large, severe bushfire in Western Australia. Methods Data collected across spatiotemporally replicated transects were used to estimate probabilities of occupancy and abundance, and to evaluate the influence of covariates. Key results Quokka abundance was reduced to 16% of pre-fire levels, with distances up to 74 km separating subpopulations. Recolonising quokkas occupied habitat in parts of the landscape that had retained some vertical vegetation structure and contained a sedge-dominated understorey, and where damage by feral pigs was low. This coincided with topographic refugia that consisted of deep, mesic riparian systems or perched wetland systems. After 5 years, abundance had increased to 46% of pre-fire levels, with distances of 5–30 km separating subpopulations. Conclusion Quokka recovery rate is slower than expected, and the metapopulation remains vulnerable to further fragmentation arising from disturbances that affect habitat patch suitability and movement corridors. Implications Proactive protection of refugia and spatiotemporal habitat connectivity within and surrounding the fire scar is critical for metapopulation recovery.

Evidence of Resident Mountain Lions (Puma concolor) on the San Pedro Riparian National Conservation Area (Arizona, USA)

The San Pedro Riparian National Conservation Area (SPRNCA) protects approximately 60 linear kilometers (km) of the San Pedro River within the Madrean Sky Islands region of southeastern Arizona. This cottonwood-willow (Populus fremontii-Salix gooddingii) gallery forest habitat with perennial surface flow is unique from the Chihuahuan mesquite desert and supports a wide diversity of plant and animal life. Mountain lions (Puma concolor) were hypothesized to use the SPRNCA as a temporary habitat while moving between neighboring mountain ranges. Using remote camera traps located on desert washes that drain the Huachuca Mountains, we demonstrated that mountain lions use the riparian corridor as part of their resident home range. We recorded 53 independent observations (mean of 1.47 observations per 100 trap nights) of mountain lions with at least 30 minutes between sightings during our study between September 2019 and May 2021. Mountain lions were found using riparian habitat in all seasons and photos were taken of young kittens within 0.3 km of the San Pedro River. Preferred prey species (Coue's white-tailed deer [Odocoileus virginianus couesi] and javelina [Pecari tajacu]) have been observed often within the SPRNCA. Future research should explore the connectivity and metapopulation structure of mountain lions within the SPRNCA and neighboring mountain ranges.

Catch Effectiveness Revealed by Site-Related Differences in Capture-Mark-Recapture Methods: A Butterfly Metapopulation Study.

Understanding metapopulation structures is very important in the context of ecological studies and conservation. Crucial in this respect are the abundances of both the whole metapopulation and its constituent subpopulations. In recent decades, capture-mark-recapture studies have been considered the most reliable means of calculating such abundances. In butterfly studies, individual insects are usually caught with an entomological net. But the effectiveness of this method can vary for a number of reasons: differences between fieldworkers, in time, between sites etc. This article analyses catch effectiveness data with respect to two subpopulations of the Apollo butterfly (Parnassius apollo) metapopulation in the Pieniny National Park (Polish Carpathians). The results show that this parameter varied significantly between sites, probably because of differences in microrelief and plant cover. In addition, a method is proposed that will include information on catch effectiveness for estimating the sizes of particular subpopulations and will help to elucidate the structure of the entire metapopulation.

Monitoring genetic diversity with new indicators applied to an alpine freshwater top predator.

Genetic diversity is the basis for population adaptation and long-term survival, yet rarely considered in biodiversity monitoring. One key issue is the need for useful and straightforward indicators of genetic diversity. We monitored genetic diversity over 40 years (1970-2010) in metapopulations of brown trout (Salmo trutta) inhabiting 27 small mountain lakes representing 10 lake systems in central Sweden using >1200 fish per time point. We tested six newly proposed indicators; three were designed for broad, international use in the UN Convention on Biological Diversity (CBD) and are currently applied in several countries. The other three were recently elaborated for national use by a Swedish science-management effort and applied for the first time here. The Swedish indicators use molecular genetic data to monitor genetic diversity within and between populations (indicators ΔH and ΔFST , respectively) and assess the effective population size (Ne -indicator). We identified 29 genetically distinct populations, all retained over time. Twelve of the 27 lakes harboured more than one population indicating that brown trout biodiversity hidden as cryptic, sympatric populations are more common than recognized. The Ne indicator showed values below the threshold (Ne ≤ 500) in 20 populations with five showing Ne < 100. Statistically significant genetic diversity reductions occurred in several populations. Metapopulation structure appears to buffer against diversity loss; applying the indicators to metapopulations suggest mostly acceptable rates of change in all but one system. The CBD indicators agreed with the Swedish ones but provided less detail. All these indicators are appropriate for managers to initiate monitoring of genetic biodiversity.

Recruitment patterns in Mexican geoduck (Panopea spp.) populations: Reconstruction from age structure and mortality parameters

The historic recruitment patterns of four populations of geoduck clams, Panopea generosa and P. globosa in northwest Mexico were analyzed by estimating a relative recruitment index (RRI) built from the age structure and mortality parameters. The RRI is a proportion of the strength of the year-class and is used as a measure of past recruitment intensities. Two recruitment patterns were observed: a) recruitments were relatively constant over time in the Punta Canoas and Puerto Peñasco populations, and b) recruitments occurred in erratic but strong pulses in the Bahía Magdalena and San Felipe populations; both of which were clearly dominant in year-classes 1988 and 1989. These differences are consistent with a strong metapopulational structure and with local conditions having an important role in recruitment regulation, thus suggesting the need to consider this structure in the design of management strategies to maintain sustainable fisheries. In particular, monitoring age classes may prove useful in identifying early changes in the recruitment patterns that may enable active management for each population.

Connectivity modelling informs metapopulation structure and conservation priorities for a reef‐building species

AbstractAimIn coastal marine systems, biogenic reef‐building species have great importance for conservation as they provide habitat for a wide range of species, promoting biodiversity, ecosystem functioning and services. Biogenic reef persistence and recovery from perturbations depend on recolonization by new recruits. Characterizing larval dispersal among distant reefs is key to understanding how connectivity shapes metapopulation structure and determines network coherence; all of which are of critical importance for effective conservation.LocationNortheast Atlantic coast and western English Channel, France.MethodsWe used a biophysical transport model to simulate larval dispersal of the reef‐building polychaete Sabellaria alveolata. We combined dispersal modelling and network analysis into a framework aiming to identify key reef areas and critical dispersal pathways, whose presence in the network is vital to its overall coherence. We evaluated changes in dispersal pathways constrained by different connectivity thresholds, i.e., minimum dispersal rate for the presence of a connection. We tested scenarios of sequential loss of reefs: randomly, by habitat quality (a score for reef status and occupancy in an area) or by betweenness centrality metric (BC; quantifying the proportion of shortest paths connecting all areas that are passing through any given area).ResultsWe found that the network of S. alveolata reefs forms two main regional clusters, the Atlantic coast and the English Channel, which are connected only through weak sporadic dispersal events. Within each cluster, the network is characterized by relatively high connectivity among neighbouring areas with reefs, maintained even under higher connectivity thresholds. Simulating scenarios of sequential loss of reefs further identified high centrality reefs, those with highest BC values, key to network coherence.Main conclusionsEffective conservation of this important reef habitat requires a network of protected areas designed to sustain a combination of locally important source reefs, and those that act as stepping stones connecting distant reefs.

Examining the impact of ICU population interaction structure on modeled colonization dynamics of Staphylococcus aureus.

Complex transmission models of healthcare-associated infections provide insight for hospital epidemiology and infection control efforts, but they are difficult to implement and come at high computational costs. Structuring more simplified models to incorporate the heterogeneity of the intensive care unit (ICU) patient-provider interactions, we explore how methicillin-resistant Staphylococcus aureus (MRSA) dynamics and acquisitions may be better represented and approximated. Using a stochastic compartmental model of an 18-bed ICU, we compared the rates of MRSA acquisition across three ICU population interaction structures: a model with nurses and physicians as a single staff type (SST), a model with separate staff types for nurses and physicians (Nurse-MD model), and a Metapopulation model where each nurse was assigned a group of patients. The proportion of time spent with the assigned patient group (γ) within the Metapopulation model was also varied. The SST, Nurse-MD, and Metapopulation models had a mean of 40.6, 32.2 and 19.6 annual MRSA acquisitions respectively. All models were sensitive to the same parameters in the same direction, although the Metapopulation model was less sensitive. The number of acquisitions varied non-linearly by values of γ, with values below 0.40 resembling the Nurse-MD model, while values above that converged toward the Metapopulation structure. Inclusion of complex population interactions within a modeled hospital ICU has considerable impact on model results, with the SST model having more than double the acquisition rate of the more structured metapopulation model. While the direction of parameter sensitivity remained the same, the magnitude of these differences varied, producing different colonization rates across relatively similar populations. The non-linearity of the model's response to differing values of a parameter gamma (γ) suggests simple model approximations are appropriate in only a narrow space of relatively dispersed nursing assignments. Simplifying assumptions around how a hospital population is modeled, especially assuming random mixing, may overestimate infection rates and the impact of interventions. In many, if not most, cases more complex models that represent population mixing with higher granularity are justified.

Modelling the responses of partially migratory metapopulations to changing seasonal migration rates: From theory to data.

Among‐individual and within‐individual variation in expression of seasonal migration versus residence is widespread in nature and could substantially affect the dynamics of partially migratory metapopulations inhabiting seasonally and spatially structured environments. However, such variation has rarely been explicitly incorporated into metapopulation dynamic models for partially migratory systems. We, therefore, lack general frameworks that can identify how variable seasonal movements, and associated season‐ and location‐specific vital rates, can control system persistence.We constructed a novel conceptual framework that captures full‐annual‐cycle dynamics and key dimensions of metapopulation structure for partially migratory species inhabiting seasonal environments. We conceptualize among‐individual variation in seasonal migration as two variable vital rates: seasonal movement probability and associated movement survival probability. We conceptualize three levels of within‐individual variation (i.e. plasticity), representing seasonal or annual variation in seasonal migration or lifelong fixed strategies. We formulate these concepts as a general matrix model, which is customizable for diverse life‐histories and seasonal landscapes.To illustrate how variable seasonal migration can affect metapopulation growth rate, demographic structure and vital rate elasticities, we parameterize our general models for hypothetical short‐ and longer‐lived species. Analyses illustrate that elasticities of seasonal movement probability and associated survival probability can sometimes equal or exceed those of vital rates typically understood to substantially influence metapopulation dynamics (i.e. seasonal survival probability or fecundity), that elasticities can vary non‐linearly, and that metapopulation outcomes depend on the level of within‐individual plasticity.We illustrate how our general framework can be applied to evaluate the consequences of variable and changing seasonal movement probability by parameterizing our models for a real partially migratory metapopulation of European shags Gulosus aristotelis assuming lifelong fixed strategies. Given observed conditions, metapopulation growth rate was most elastic to breeding season adult survival of the resident fraction in the dominant population. However, given doubled seasonal movement probability, variation in survival during movement would become the primary driver of metapopulation dynamics.Our general conceptual and matrix model frameworks, and illustrative analyses, thereby highlight complex ways in which structured variation in seasonal migration can influence dynamics of partially migratory metapopulations, and pave the way for diverse future theoretical and empirical advances.

Invasive species fouling Perna perna (Bivalvia: Mytilidae) mussel farms

Invasive, fouling species increase management costs and reduce mussel growth, which jeopardizes mariculture. We studied the distribution of eight invasive species in Santa Catarina, the leading mussel producer in Brazil. Our goals were to determine their spatial distribution and prevalence on farm structures (buoys, long lines, and mussel socks), as well as understand the relevance of propagule pressure (recruitment), port distance, and area of the farm in this distribution. Although present in all sites, adult and recruits distribution were spatially restricted, showing that species might have a metapopulation structure. The most prevalent species were the ascidian Styela plicata, the barnacle Megabalanus coccopoma, the bryozoan Schizoporella errata, and the polychaete Branchiomma luctuosum. Recruitment was the main driver of three species distribution while distance to port explained only one species distribution. Based on those results, we discuss policy options, management, and regulation enforcement, that can be used in the mussel aquaculture elsewhere.

Life history adaptations of Carabus populations in a suburban park: A capture-recapture case study

A two seasons capture-recapture study was preformed between 2016 and 2017, focusing on the Carabus species living in a suburban park in Budapest, Hungary. Eighty-four live-capture non-baited pitfall traps were placed in a grid covering an area of 567 m 2 . Five Carabus species were captured in the park from the nine species in the potential species pool. The most numerous were C. scheidleri , C. ulrichii and C. coriaceus . C. convexus and C. intricatus were captured only a few times. All Carabus species were individually marked and released. We experienced high fluctuation in the estimated population size of C. scheidleri and C. ulrichii, the two most abundant species. The marking technique made possible to detect that the two dominant species overwinter both as larvae and as adults, and thus share remarkably similar life histories. Similar habitat preference, life cycle and low dispersal power sets stage for potential competition between the two species. Due to population sizes below viability limit and the potential for competitive interactions, we presume that a larger network of metapopulation structure makes it possible that these populations persist in a suburban park. The results indicate that urban parks, if they are sufficiently connected to other suitable habitat patches, can have a significant importance in preserving large bodied predatory Carabus species.

Comparison of Indices to Infer Population Dynamics of Black Brant

Abstract To aid managers in assessing status of Pacific black brant Branta bernicla nigricans (hereafter brant), I examined pre-existing long-term data series from summer, fall staging, and wintering areas to infer overall population processes and assessed the utility of the various data sources. Variation in demographic parameters measured in subarctic and Arctic locations suggests some form of metapopulation structure likely exists for brant. I used serial autocorrelation coefficients to assess the ability of various indices to track population processes. Based on this approach, the Lincoln–Petersen estimator and the fall aerial survey estimate partitioned using age ratios of staging brant at Izembek Lagoon, Alaska, appear to be the best indicators. However, these two indexes show different trends for the overall brant population. The Lincoln–Petersen estimates showed biologically implausible changes in size among sequential years, whereas the fall Izembek index did not. Annual estimates of survival and productivity fit the patterns of annual variation in the fall Izembek index better than the Lincoln–Petersen estimates. I conclude that the fall age–partitioned Izembek Lagoon index appears to be the best for tracking population processes in brant.

Gene flow in a pioneer plant metapopulation (Myricaria germanica) at the catchment scale in a fragmented alpine river system

River alterations for natural hazard mitigation and land reclamation result in habitat decline and fragmentation for riparian plant species. Extreme events such as floods are responsible for additional local species loss or population decline. Tributaries might provide refugia and subsequent source populations for the colonization of downstream sites in connected riverine networks with metapopulations of plant species. In this study, we analyzed the metapopulation structure of the endangered riparian shrub species Myricaria germanica along the river Isel, Austria, which is part of the Natura 2000 network, and its tributaries. The use of 22 microsatellite markers allowed us to assess the role of tributaries and single populations as well as gene flow up- and downstream. The analysis of 1307 individuals from 45 sites shows the influence of tributaries to the genetic diversity at Isel and no overall isolation by distance pattern. Ongoing bidirectional gene flow is revealed by the detection of first-generation migrants in populations of all tributaries as well as the river Isel, supporting upstream dispersal by wind (seeds) or animals (seeds and pollen). However, some populations display significant population declines and high inbreeding, and recent migration rates are non-significant or low. The genetic pattern at the mouth of river Schwarzach into Isel and shortly thereafter river Kalserbach supports the finding that geographically close populations remain connected and that tributaries can form important refugia for M. germanica in the dynamic riverine network. Conservation and mitigation measures should therefore focus on providing sufficient habitat along tributaries of various size allowing pioneer plants to cope with extreme events in the main channel, especially as they are expected to be more frequent under changing climate.

Experimental evolution reveals differential evolutionary trajectories in male and female activity levels in response to sexual selection and metapopulation structure.

Behavior is central to interactions with the environment and thus has significant consequences for individual fitness. Sexual selection and demographic processes have been shown to independently shape behavioral evolution. Although some studies have tested the simultaneous effects of these forces, no studies have investigated their interplay in behavioral evolution. We applied experimental evolution in the seed beetle Callosobruchus maculatus to investigate, for the first time, the interactive effects of sexual selection intensity (high [polygamy] vs. minimal [enforced monogamy]) and metapopulation structure (yes/no) on the evolution of movement activity, a crucial behavior involved in multiples functions (e.g., dispersal, predator avoidance, or resource acquisition) and thus, closely related to fitness. We found that the interactive effects of the selection regimes did not affect individual activity, which was assayed under two different environments (absence vs. presence of conspecific cues from both sexes). However, contrasting selection regimes led to sex‐ and context‐dependent divergence in activity. The relaxation of sexual selection favored an increase in female, but not male, movement activity that was consistent between environmental contexts. In contrast, selection associated with the presence/absence of metapopulation structure led to context‐dependent responses only in male activity. In environments containing cues from conspecifics, males from selection lines under population subdivision showed increased levels of activity compared to those assayed in an environment devoid of conspecifics cues, whereas the opposite was true for males from panmictic lines. These results underscore that both the effects of sexual selection and population spatial structure may be crucial in shaping sex‐specific behavioral evolution.

Local population collapse of Ross's and lesser snow geese driven by failing recruitment and diminished philopatry

Dynamics of free‐ranging animal populations can result from complex interplays of survival, recruitment and movement. Yet incomplete understanding of demography impedes conservation strategies intended to modify population dynamics of focal species. We estimated survival and per capita production of young, as well as emigration and immigration, from 1997 to 2017 in Ross's goose Anser rossii and lesser snow goose Anser caerulescens caerulescens, which are sympatric species of migratory birds that nest in the central Canadian Arctic at one of the largest breeding colonies in North America. We formed age‐structured integrated population models (IPMs) for each species that jointly analyzed live and dead encounter data as well as breeding adult population size and fecundity data to understand drivers of population dynamics. We compared the demography between species because both species increased during the 1990s and early 2000s yet thereafter snow geese declined, while Ross's geese continued to increase, then stabilized and similarly declined. Declines in Ross's and snow goose populations were caused by reduced per capita production of young, and juvenile survival, as well as increased adult and juvenile emigration. Stronger declines in juvenile survival in snow geese explain their earlier population decline compared to Ross's geese. Despite the divergence in population trends in Ross's and snow geese, we found strong synchrony in demographic rates which suggested substantial emigration from this colony and similar responses to environmental conditions. Direct estimation of demographic patterns in the IPM framework permitted hypothesis testing and inference about the role of immigration, even though immigrant sources were unsampled. We provide a novel m‐array implementation specific to a multi‐state Burnham model which greatly improved computational efficiency and convergence of posterior estimates. Our findings are an important reminder of the role that permanent movements can play in animal demography and metapopulation structure.

Understanding the biology of species' ranges: when and how does evolution change the rules of ecological engagement?

Understanding processes that limit species' ranges has been a core issue in ecology and evolutionary biology for many decades, and has become increasingly important given the need to predict the responses of biological communities to rapid environmental change. However, we still have a poor understanding of evolution at range limits and its capacity to change the ecological 'rules of engagement' that define these communities, as well as the time frame over which this occurs. Here we link papers in the current volume to some key concepts involved in the interactions between evolutionary and ecological processes at species' margins. In particular, we separate hypotheses about species' margins that focus on hard evolutionary limits, which determine how genotypes interact with their environment, from those concerned with soft evolutionary limits, which determine where and when local adaptation can persist in space and time. We show how theoretical models and empirical studies highlight conditions under which gene flow can expand local limits as well as contain them. In doing so, we emphasize the complex interplay between selection, demography and population structure throughout a species' geographical and ecological range that determines its persistence in biological communities. However, despite some impressively detailed studies on range limits, particularly in invertebrates and plants, few generalizations have emerged that can predict evolutionary responses at ecological margins. We outline some directions for future work such as considering the impact of structural genetic variants and metapopulation structure on limits, and the interaction between range limits and the evolution of mating systems and non-random dispersal. This article is part of the theme issue 'Species' ranges in the face of changing environments (Part II)'.

On mobility trends analysis of COVID-19 dissemination in Mexico City.

This work presents a tool for forecasting the spread of the new coronavirus in Mexico City, which is based on a mathematical model with a metapopulation structure that uses Bayesian statistics and is inspired by a data-driven approach. The daily mobility of people in Mexico City is mathematically represented by an origin-destination matrix using the open mobility data from Google and the Transportation Mexican Survey. This matrix is incorporated in a compartmental model. We calibrate the model against borough-level incidence data collected between 27 February 2020 and 27 October 2020, while using Bayesian inference to estimate critical epidemiological characteristics associated with the coronavirus spread. Given that working with metapopulation models leads to rather high computational time consumption, and parameter estimation of these models may lead to high memory RAM consumption, we do a clustering analysis that is based on mobility trends to work on these clusters of borough separately instead of taken all of the boroughs together at once. This clustering analysis can be implemented in smaller or larger scales in different parts of the world. In addition, this clustering analysis is divided into the phases that the government of Mexico City has set up to restrict individual movement in the city. We also calculate the reproductive number in Mexico City using the next generation operator method and the inferred model parameters obtaining that this threshold is in the interval (1.2713, 1.3054). Our analysis of mobility trends can be helpful when making public health decisions.

Close-kin mark–recapture abundance estimation: practical insights and lessons learned

Abstract We present practical lessons learned from applying the recent close-kin mark–recapture (CKMR) abundance estimation method to thornback ray (Raja clavata). For CKMR, related individuals are identified from their genotypes and their number and pattern is used for abundance estimation. We genotyped over 7000 individuals collected in the Bay of Biscay using Single Nucleotide Polymorphism (SNP) markers finding 99 parent–offspring pairs. The estimated number of adult thornback rays in the central Bay of Biscay was around 135000 (CV 0.19) in 2013. In total, four lessons were drawn: (i) CKMR helps identifying metapopulation structure, which if ignored might affect abundance estimates and/or time trends. There was strong evidence for two distinct local populations of thornback ray with no demographic connectivity. (ii) Demographic sample composition can affect precision and needs to include a range of birth years, which turned out to be difficult for thornback ray. (iii) Reasonable age information for potential offspring is essential. (iv) The sex of potential parents is needed and might be identified from sex-related SNPs. Reliable abundance estimation by CKMR appears feasible for a wide range of species provided that: sampling adequately covers potential local population structure, has appropriate demographic composition, and the age of potential offspring is reasonably well-known.