Extinction-recolonization Dynamics Research Articles

Quantifying dispersal between two colonies of northern elephant seals across 17 birth cohorts.

Dispersal drives extinction-recolonization dynamics of metapopulations and is necessary for endangered species to recolonize former ranges. Yet few studies quantify dispersal and even fewer examine consistency of dispersal over many years. The northern elephant seal (Mirounga angustirostris) provides an example of the importance of dispersal. It quickly recolonized its full range after near extirpation by 19th century hunting, and though dispersal was observed it was not quantified. Here we enumerate lifetime dispersal events among females marked as pups at two colonies during 1994-2010, then correct for detection biases to estimate bidirectional dispersal rates. An average of 16% of females born at the Piedras Blancas colony dispersed northward 200 km to breed at Año Nuevo, while 8.0% of those born at Año Nuevo dispersed southward to Piedras Blancas. The northward rate fluctuated considerably but was higher than southward in 15 of 17 cohorts. The population at Piedras Blancas expanded 15-fold during the study, while Año Nuevo's declined slightly, but the expectation that seals would emigrate away from high density colonies was not supported. During the 1990s, dispersal was higher away from the small colony toward the large. Moreover, cohorts born later at Piedras Blancas, when the colony had grown, dispersed no more than early cohorts. Consistently high natal dispersal in northern elephant seals means the population must be considered a single large unit in terms of response to environmental change. High dispersal was fortuitous to the past recovery of the species, and continued dispersal means elephant seals will likely expand their range further.

Natural mega disturbances drive spatial and temporal changes in diversity and genetic structure on the toadfish Aphos porosus

Natural disturbances can modify extinction-colonization dynamics, driving changes in the genetic diversity and structure of marine populations. Along Chilean coast (36°S, 73°W), a strong hypoxic-upwelling event in 2008, and a mega earthquake-tsunami in 2010 caused mass mortality within the Aphos porosus population, which is a vulnerable species with low dispersal potential. We evaluated the effects of these two major disturbances on the diversity and spatial-temporal genetic structure of Aphos porosus in two neighboring areas that were impacted on different levels (High level: Coliumo Bay; Low level: Itata Shelf). Thirteen microsatellites (from 2008 to 2015) amplified in individuals collected from both locations were used to evaluate the effects of the two disturbances. Results showed that after the strong hypoxic-upwelling event and the mega earthquake-tsunami, Aphos porosus populations exhibited lower genetic diversity and less effective population sizes (Ne < 20), as well as asymmetries in migration and spatial-temporal genetic structure. These findings suggest a rise in extinction-recolonization dynamics in local Aphos porosus populations after the disturbances, which led to a loss of local genetic diversity (mainly in Coliumo Bay area impacted the most), and to greater spatial-temporal genetic structure caused by drift and gene flow. Our results suggest that continuous genetic monitoring is needed in order to assess potential risks for Aphos porosus in light of new natural and anthropogenic disturbances.

Phylodynamics reveals extinction-recolonization dynamics underpin apparently endemic vampire bat rabies in Costa Rica.

Variation in disease incidence in wildlife is often assumed to reflect environmental or demographic changes acting on an endemic pathogen. However, apparent endemicity might instead arise from spatial processes that are challenging to identify from traditional data sources including time series and field studies. Here, we analysed longitudinal sequence data collected from rabies virus outbreaks over 14 years in Costa Rica, a Central American country that has recorded continuous vampire bat-transmitted rabies outbreaks in humans and livestock since 1985. We identified five phylogenetically distinct lineages which shared most recent common ancestors with viruses from North and South America. Bayesian phylogeographic reconstructions supported bidirectional viral dispersals involving countries to the north and south of Costa Rica at different time points. Within Costa Rica, viruses showed little contemporaneous spatial overlap and no lineage was detected across all years of surveillance. Statistical models suggested that lineage disappearances were more likely to be explained by viral extinctions than undetected viral circulation. Our results highlight the importance of international viral dispersal for shaping the burden of rabies in Costa Rica, suggest a Central American corridor of rabies virus invasions between continents, and show that apparent disease endemicity may arise through recurrent pathogen extinctions and reinvasions which can be readily detected in relatively small datasets by joining phylodynamic and modelling approaches.

Heterogeneity in local density allows a positive evolutionary relationship between self-fertilisation and dispersal.

Despite empirical evidence for a positive relationship between dispersal and self-fertilization (selfing), theoretical work predicts that these traits should always be negatively correlated, and the Good Coloniser Syndrome of high dispersal and selfing (Cf. Baker's Law) should not evolve. Critically, previous work assumes that adult density is spatiotemporally homogeneous, so selfing results in identical offspring production for all patches, eliminating the benefit of dispersal for escaping from local resource competition. We investigate the joint evolution of dispersal and selfing in a demographically structured metapopulation model where local density is spatiotemporally heterogeneous due to extinction-recolonization dynamics. Selfing alleviates outcrossing failure due to low local density (an Allee effect) while dispersal alleviates competition through dispersal of propagules from high- to low-density patches. Because local density is spatiotemporally heterogeneous in our model, selfing does not eliminate heterogeneity in competition, so dispersal remains beneficial even under full selfing. Hence the Good Coloniser Syndrome is evolutionarily stable under a broad range of conditions, and both negative and positive relationships between dispersal and selfing are possible, depending on the environment. Our model thus accommodates positive empirical relationships between dispersal and selfing not predicted by previous theoretical work and provides additional explanations for negative relationships.

Fugitive Coexistence Mediated by Evolutionary Lag in Local Adaptation in Metapopulations

Extinction—recolonization dynamics is known to promote “fugitive coexistence” in patchy environments: a species that is an inferior competitor but a better colonizer may persist by exploiting the period between its colonization of a patch and the arrival of a superior competitor. Here I use a simple model to demonstrate the plausibility of a different type of fugitive coexistence. I show that, under some circumstances, a “jack of all trades” plastic species can persist despite competition from an adaptable species that has the genetic potential to adapt locally and outcompete the plastic species in every patch. This persistence can be mediated by two forces that impede local adaptation: gene flow and extinction—recolonization dynamics. In the latter case, the persistence of the plastic species is of a fugitive nature; however, it is not mediated by an earlier colonization. Rather, it relies on the fact that, following recolonization, the adaptable species is often locally maladapted. This opens a time window for the plastic species to multiple and produce propagules before the other species becomes locally adapted, and thus competitively superior.

Phylogeography of Quercus aquifolioides provides novel insights into the Neogene history of a major global hotspot of plant diversity in south‐west China

AbstractAimHotspots of biodiversity are often associated with areas that have undergone orogenic activity during recent geological history. Mountain uplifts are known to catalyse species radiation but their impact on evolutionarily stable taxa such as many trees remains little understood. The oak Quercus aquifolioides is endemic to yet widely distributed across the Hengduanshan Biodiversity Hotspot in the Eastern Himalayas. Here, we investigate how the region's Neogene and Quaternary history has driven the species' past population dynamics and the resulting extant patterns of intraspecific diversity.LocationHengduanshan Biodiversity Hotspot in SW China.MethodsWe sampled 58 populations throughout the species range and genotyped a total of 959 individuals at four chloroplast DNA fragments and 11 nuclear microsatellite loci. Phylogenetic reconstructions, molecular dating techniques and ancestral area reconstructions were used in combination with population genetic statistics to infer the biogeographical history of Q. aquifolioides. The phylogeographical study was complemented by a survey of fossil records and a niche modelling exercise.ResultsCombined molecular and fossil evidence indicates that Q. aquifolioides descended during the late Miocene from the central Qinghai‐Tibet Plateau into Tibet and the western Sichuan Plateau, and from there, into the area of highest endemism in the Hengduan Mountains sensu lato. Great apparent population stability and a haplotype ‘radiation’ in this area contrasted with marked extinction–recolonization dynamics and reduced population diversity in Tibet. We found evidence for extremely limited seed gene flow but extensive pollen gene flow (global FST: cpDNA = 0.98, nSSR = 0.07) with signals of asymmetric pollen dispersal from the Hengduan Mountains into Tibet.Main conclusionOur results provide insights of unprecedented detail into the ancient biogeographical history of the Hengduanshan Biodiversity Hotspot, suggesting that past environmental changes in the region may have catalysed radiative diversifications within species much in the same way as among species.

Deep and wide valleys drive nested phylogeographic patterns across a montane bird community.

Montane species distributions interrupted by valleys can lead to range fragmentation, differentiation and ultimately speciation. Paleoclimatic fluctuations may accentuate or reduce such diversification by temporally altering the extent of montane habitat and may affect species differentially. We examined how an entire montane bird community of the Western Ghats--a linear, coastal tropical mountain range--responds to topographic valleys that host different habitats. Using genetic data from 23 species (356 individuals) collected across nine locations, we examined if different species in the community reveal spatial concordance in population differentiation, and whether the timing of these divergences correlate with climatic events. Our results reveal a nested effect of valleys, with several species (10 of 23) demonstrating the oldest divergences associated with the widest and deepest valley in the mountain range, the Palghat Gap. Further, a subset of these 10 species revealed younger divergences across shallower, narrower valleys. We recovered discordant divergence times for all valley-affected montane birds, mostly in the Pleistocene, supporting the Pliestocene-pump hypotheses and highlighting the role of climatic fluctuations during this period in driving species evolution. A majority of species remain unaffected by valleys, perhaps owing to geneflow or extinction-recolonization dynamics. Studying almost the entire community allowed us to uncover a range of species' responses, including some generalizable and other unpredicted patterns.

Increases and decreases in network synchrony associated with local population extinction and recolonization

Synchronous population dynamics, a positive correlation in growth rates among populations, is of interest from basic and applied perspectives. Synchronous dynamics are ubiquitous in nature thus understanding the mechanisms producing synchrony is fundamental. Population networks with synchronous dynamics have shorter persistence times than asynchronous networks, thus understanding its sources may aid conservation. Previous research has shown that the extinction and recolonization of local populations within a spatial population network produces a decrease in synchrony; however, models investigating extinction alone have shown increases in synchrony and the potential for increased network wide extinction risk. Here, I investigated these contrasting results. At low population growth rates, r=1.1, the extinction and recolonization of a local population increased the synchrony of surrounding populations. Also in contrast to previous results, at higher growth rates, r>2.1, extinction–recolonization dynamics resulted in a range of results – increasing, decreasing, and no change in synchrony. In all cases, the impact of extinction and recolonization dynamics on synchrony depended on whether dispersal was local or global, the population growth rate, the emigration rate, and the amount of local stochasticity. Results indicate that there is a high potential for positive feedback of local extinction and recolonization on network-wide extinction risk for patchy populations of species with low intrinsic growth rates.

Host Resistance, Population Structure and the Long-Term Persistence of Bubonic Plague: Contributions of a Modelling Approach in the Malagasy Focus

Although bubonic plague is an endemic zoonosis in many countries around the world, the factors responsible for the persistence of this highly virulent disease remain poorly known. Classically, the endemic persistence of plague is suspected to be due to the coexistence of plague resistant and plague susceptible rodents in natural foci, and/or to a metapopulation structure of reservoirs. Here, we test separately the effect of each of these factors on the long-term persistence of plague. We analyse the dynamics and equilibria of a model of plague propagation, consistent with plague ecology in Madagascar, a major focus where this disease is endemic since the 1920s in central highlands. By combining deterministic and stochastic analyses of this model, and including sensitivity analyses, we show that (i) endemicity is favoured by intermediate host population sizes, (ii) in large host populations, the presence of resistant rats is sufficient to explain long-term persistence of plague, and (iii) the metapopulation structure of susceptible host populations alone can also account for plague endemicity, thanks to both subdivision and the subsequent reduction in the size of subpopulations, and extinction-recolonization dynamics of the disease. In the light of these results, we suggest scenarios to explain the localized presence of plague in Madagascar.

Optimal life‐history schedule in a metapopulation with juvenile dispersal

Previous models have predicted that when mortality increases with age, older individuals should invest more of their resources in reproduction and produce less dispersive offspring, as both their future reproductive value and their prospect of competing with their own sib decline. Those models assumed stable population sizes. We here study for the first time the evolution of age-specific reproductive effort and of age-specific offspring dispersal rate in a metapopulation with extinction-recolonization dynamics and juvenile dispersal. Our model explores the evolutionary consequences of disequilibrium in the age structure of individuals in local populations, generated by disturbances. Life-history decisions are then shaped both by changes with age in individual performances, and by changes in ecological conditions, as young and old individuals do not live on average in the same environments. Lower juvenile dispersal favours the evolution of higher reproductive effort in young adults in a metapopulation with extinction-recolonization compared with a well-mixed population. Contrary to previous predictions for stable structured populations, we find that offspring dispersal should generally increase with maternal age. This is because young individuals, who are overrepresented in recently colonized populations, should allocate more to reproduction and less to dispersal as a strategy to exploit abundant recruitment opportunities in such populations.

Selection-Driven Extinction Dynamics for Group II Introns in Enterobacteriales

Transposable elements (TEs) are one of the major driving forces of genome evolution, raising the question of the long-term dynamics underlying their evolutionary success. Some TEs were proposed to evolve under a pattern of periodic extinctions-recolonizations, in which elements recurrently invade and quickly proliferate within their host genomes, then start to disappear until total extinction. Depending on the model, TE extinction is assumed to be driven by purifying selection against colonized host genomes (Sel-DE model) or by saturation of host genomes (Sat-DE model). Bacterial group II introns are suspected to follow an extinction-recolonization model of evolution, but whether they follow Sel-DE or Sat-DE dynamics is not known. Our analysis of almost 200 group II intron copies from 90 sequenced Enterobacteriales genomes confirms their extinction-recolonization dynamics: patchy element distributions among genera and even among strains within genera, acquisition of new group II introns through plasmids or other mobile genetic elements, and evidence for recent proliferations in some genomes. Distributions of recent and past proliferations and of their respective homing sites further provide strong support for the Sel-DE model, suggesting that group II introns are deleterious to their hosts. Overall, our observations emphasize the critical impact of host properties on TE dynamics.

Phenotypic evolution of dispersal-enhancing traits in insular voles

Evolutionary theory predicts that in metapopulations subject to rapid extinction-recolonization dynamics, natural selection should favour evolution of traits that enhance dispersal and recolonization ability. Metapopulations of field voles (Microtus agrestis) on islands in the Stockholm archipelago, Sweden, are characterized by frequent local extinction and recolonization of subpopulations. Here, we show that voles on the islands were larger and had longer feet than expected for their body size, compared with voles from the mainland; that body size and size-specific foot length increased with increasing geographical isolation and distance from mainland; and that the differences in body size and size-specific foot length were genetically based. These findings provide rare evidence for relatively recent (less than 1000 years) and rapid (corresponding to 100-250 darwins) evolution of traits facilitating dispersal and recolonization in island metapopulations.

THE RELEVANCE OF GENE FLOW IN METAPOPULATION DYNAMICS OF AN OCEANIC ISLAND ENDEMIC, OLEA EUROPAEA SUBSP. GUANCHICA

Theoretical and empirical studies suggest that geographical isolation and extinction-recolonization dynamics are two factors causing strong genetic structure in metapopulations, but their consequences in species with high dispersal abilities have not been tested at large scales. Here, we investigated the effect of population age structure and isolation by distance in the patterns of genetic diversity in a wind-pollinated, zoochorous tree (Olea europaea subsp. guanchica) sporadically affected by volcanic events across the Canarian archipelago. Genetic variation was assessed at six nuclear microsatellites (nDNA) and six chloroplast fragments (cpDNA) in nine subpopulations sampled on four oceanic islands. Subpopulations occurring on more recent substrates were more differentiated than those on older substrates, but within-subpopulation genetic diversity was not significantly different between age groups for any type of marker. Isolation-by-distance differentiation was observed for nDNA but not for cpDNA, in agreement with other metapopulation studies. Contrary to the general trend for island systems, between-island differentiation was extremely low, and lower than differentiation between subpopulations on the same island. The pollen-to-seed ratio was close to one, two orders of magnitude lower than the average estimated for other wind-pollinated, animal-dispersed plants. Our results showed that population turnover and geographical isolation increased genetic differentiation relative to an island model at equilibrium, but overall genetic structure was unexpectedly weak for a species distributed among islands. This empirical study shows that extensive gene flow, particularly mediated by seeds, can ameliorate population subdivision resulting from extinction-recolonization dynamics and isolation by distance.

Rubella metapopulation dynamics and importance of spatial coupling to the risk of congenital rubella syndrome in Peru

Rubella is generally a mild childhood disease, but infection during early pregnancy may cause spontaneous abortion or congenital rubella syndrome (CRS), which may entail a variety of birth defects. Consequently, understanding the age-structured dynamics of this infection has considerable public health value. Vaccination short of the threshold for local elimination of transmission will increase the average age of infection. Accordingly, the classic concern for this infection is the potential for vaccination to increase incidence in individuals of childbearing age. A neglected aspect of rubella dynamics is how age incidence patterns may be moulded by the spatial dynamics inherent to epidemic metapopulations. Here, we use a uniquely detailed dataset from Peru to explore the implications of this for the burden of CRS. Our results show that the risk of CRS may be particularly severe in small remote regions, a prediction at odds with expectations in the endemic situation, and with implications for the outcome of vaccination. This outcome results directly from the metapopulation context: specifically, extinction–re-colonization dynamics are crucial because they allow for significant leakage of susceptible individuals into the older age classes during inter-epidemic periods with the potential to increase CRS risk by as much as fivefold.

Spatial and temporal changes in genetic structure of greenhouse and field populations of cabbage looper,Trichoplusia ni

Trichoplusia ni is a subtropical moth that migrates annually from southern California to southern British Columbia, Canada where it invades vegetable greenhouses and field crops. The heated greenhouse environment has altered the natural extinction-recolonization dynamics of T. ni populations, and allows year-round persistence in some locations. In addition, the extensive use of the biopesticide, Bacillus thuringiensis subspecies kurstaki (Bt) in some greenhouses has selected for resistance. Here we investigated the genetic structure of T. ni populations in British Columbia greenhouses and in field populations in California and British Columbia using amplified fragment length polymorphisms (AFLP) as related to patterns of Bt resistance. The majority of British Columbia field populations were similar to the California field populations, the potential source of migrants. However populations in two geographic areas with high concentrations of greenhouses showed local genetic differentiation. Some of these populations experienced severe bottlenecks over-winter and following Bt sprays. Greenhouse populations showed a pattern of isolation by distance and a strong positive relationship between genetic differentiation and levels of Bt resistance. These patterns indicate that greenhouses that sometimes support year-round populations of T. ni and the ensuing strong bottlenecking effects following winter cleanups and Bt application cause genetic differentiation of T. ni populations. Long distance migrants to field populations contribute to genetic homogeneity of these.

Spatial population structure of a specialist leaf‐mining moth

1. The spatial structure of natural populations may profoundly influence their dynamics. Depending on the frequency of movements among local populations and the consequent balance between local and regional population processes, earlier work has attempted to classify metapopulations into clear-cut categories, ranging from patchy populations to sets of remnant populations. In an alternative, dichotomous scheme, local populations have been classified as self-sustaining populations generating a surplus of individuals (sources) and those depending on immigration for persistence (sinks). 2. In this paper, we describe the spatial population structure of the leaf-mining moth Tischeria ekebladella, a specialist herbivore of the pedunculate oak Quercus robur. We relate moth dispersal to the distribution of oaks on Wattkast, a small island (5 km(2)) off the south-western coast of Finland. 3. We build a spatially realistic metapopulation model derived from assumptions concerning the behaviour of individual moths, and show that the model is able to explain part of the variation in observed patterns of occurrence and colonization. 4. While the species was always present on large trees, a considerable proportion of the local populations associated with small oaks showed extinction-recolonization dynamics. The vast majority of moth individuals occur on large trees. 5. According to model predictions, the dominance of local vs. regional processes in tree-specific moth dynamics varies drastically across the landscape. Most local populations may be defined broadly as 'sinks', as model simulations suggest that in the absence of immigration, only the largest oaks will sustain viable moth populations. Large trees in areas of high oak density will contribute most to the overall persistence of the metapopulation by acting as sources of moths colonizing other trees. 6. No single 'metapopulation type' will suffice to describe the oak-moth system. Instead, our study supports the notion that real populations are often a mix of earlier identified categories. The level to which local populations may persist after landscape modification will vary across the landscape, and sweeping classifications of metapopulations into single categories will contribute little to understanding how individual local populations contribute to the overall persistence of the system.

Northwest passages: conservation genetics of Arctic Island wolves

Wolves in the Canadian Arctic Archipelago face several challenges to persistence: a harsh habitat, an unstable prey base, and potentially significant anthropogenic influences. These external factors, if combined with genetic constraints common to island populations, could be particularly difficult to withstand. To determine the genetic status of Arctic Island wolves, we used 14 microsatellite loci to estimate population variation and the extent of inter-island and island-mainland gene flow. All island populations were significantly less variable than mainland wolves; although inbreeding is currently insignificant, the two least variable populations, Banks and the High Arctic (Ellesmere and Devon Islands), showed genetic signatures of recent population declines. Recovery after a bottleneck appears to result, in large part, via recolonization from other islands. These extinction-recolonization dynamics, and the degree of similarity among island wolves revealed by Bayesian clustering, suggest that Arctic Island wolves function as a metapopulation. Persistence of the metapopulation may be supported by periodic migration from mainland populations, occurring primarily through two corridors: Baffin Island in the Eastern Arctic, and Victoria Island in the Western Arctic. This gene flow could be compromised or eliminated by loss—due to climatic warming or increased human activity—of sea ice in the Northwest Passage.

CHANGES IN FROG AND TOAD POPULATIONS OVER 30 YEARS IN NEW YORK STATE

Lack of historical data against which to measure population trends greatly hampers understanding the status of amphibians. In 2001–2002 we resurveyed a hitherto unexamined baseline of monitoring data established in 1973–1980 at some 300 sites in western, central, and northern New York State, USA, and contrasted population transitions with environmental conditions to identify correlates of population change in American toads (Bufo americanus), northern spring peepers (Pseudacris crucifer), western chorus frogs (Pseudacris triseriata), leopard frogs (Rana pipiens), and wood frogs (Rana sylvatica). At the regional level, loss of habitats along roadsides has been substantial (minimally 7– 12% of sites), yet within remaining wetlands, populations of most anurans have not declined. At the local level, population disappearance was associated with elevated levels of acid deposition (in American toad, spring peeper, western chorus frog, and leopard frog), urban development (American toad and spring peeper), increased forest cover (western chorus frog), and high‐intensity agriculture (spring peeper); whereas population persistence was associated with increased deciduous forest cover (American toad, spring peeper, and wood frog) and low‐intensity agriculture (American toad and western chorus frog). Habitat configurations at surprisingly large spatial scales (5–10 km from surveyed populations) were most closely associated with transitions in local anuran populations, implying that large‐scale extinction–recolonization dynamics influence population transitions, a result land managers should consider in conservation planning.

Colonization‐extinction and patch dynamics of the perennial riparian plant,Silene tatarica

1 Although the concept of metapopulation is central to modern conservation biology, plant population biologists have divergent views concerning the importance of metapopulation dynamics. 2 We studied the patch structure and colonization-extinction dynamics of Silene tatarica by mapping its distribution along a 43-km stretch of riverside subjected to annual flood disturbances. Plants were grouped into patches that were surveyed annually. The effect of spatial scale on dynamics was evaluated by varying the interplant separation used to determine grouping from 5 to 200 m. Using the 5-m criterion, the number of patches varied from 703 to 854 over the 5 years of the study. 3 New patches were colonized by a few individuals and located on average 50 m away from the closest old patch. Recolonization of extinct patches was very rare. Small patches had the highest risk of extinction (5%) and, although floods can destroy even large populations, no large patches with flowering individuals became extinct. 4 Elasticity analysis indicated that the survival of patches made a much greater contribution to patch dynamics than the production of new patches. Increasing patch scale decreased the rates of colonization and extinction as well as the projected finite rates of increase in patch number, but elasticities remained invariant. 5 The river dynamics both create space for colonization and cause local extinctions, especially of small patches. The short-term dynamics of S. tatarica depend primarily on local dynamics but, in the long run, the species will track the availability of habitat, and its persistence will depend on a positive balance between colonization and extinction. 6 This species from a transient environment does not exhibit the extinction-recolonization dynamics predicted for metapopulations at equilibrium. The rate of the dynamics of plant species in relation to the rate of habitat changes may be one of the key determinants of their regional dynamics.

Metapopulation ecology in the sea: from Levins' model to marine ecology and fisheries science

AbstractMarine and fisheries scientists are increasingly using metapopulation concepts to better understand and model their focal systems. Consequently, they are considering what defines a metapopulation. One perspective on this question emphasizes the importance of extinction probability in local populations. This view probably stems from the focus on extinction in Levins' original metapopulation model, but places unnecessary emphasis on extinction–recolonization dynamics. Metapopulation models with more complex structure than Levins' patch‐occupancy model and its variants allow a broader range of population phenomena to be examined, such as changes in population size, age structure and genetic structure. Analyses along these lines are critical in fisheries science, where presence–absence resolution is far too coarse to understand stock dynamics in a meaningful way. These more detailed investigations can, but need not, aim to assess extinction risk or deal with extinction‐prone local populations. Therefore, we emphasize the coupling of spatial scales as the defining feature of metapopulations. It is the degree of demographic connectivity that characterizes metapopulations, with the dynamics of local populations strongly dependent upon local demographic processes, but also influenced by a nontrivial element of external replenishment. Therefore, estimating rates of interpopulation exchange must be a research priority. We contrast metapopulations with other spatially structured populations that differ in the degree of local closure of their component populations. We conclude with consideration of the implications of metapopulation structure for spatially explicit management, particularly the design of marine protected area networks.