Inferring extinction from a sighting record

The extinctions of plant and animal species are almost never observed directly, but must be inferred from sighting records. This paper reviews some methods for statistical inference about the extinction of a single species based on a record of its sightings.     

BIODIVERSITY RESEARCH: When is a species really extinct? Testing extinction inference from a sighting record to inform conservation assessment

Aim The global extinction of a species typically represents the end point in a series of population extinctions, during which unique evolutionary history is lost at every stage. Insight into the process of extinction can provide the means to identify species at high risk, but the number of extinctions being identified languishes far behind true totals. More proactive ways of inferring extinction from limited data are required. Location Historic sightings, collections and specimen data from Australia and Asia. Method We used a technique called optimal linear estimation to analyse the sightings record of mammal and bird species of varying ecology, life history and population demography. The mammal species chosen were all considered regionally extinct in the literature, while the bird species chosen had all been highlighted as candidates for the new IUCN Red List category flag: Critically Endangered (Possibly Extinct). Results Nine of the ten mammal species were predicted to be probably extinct, but only two with 95% certainty. Seven of the ten bird species were predicted to be probably extinct, four with 95% certainty. Main conclusions Superficially, determining whether a species is extinct might seem a simple task, whereby we either find a species extant, or it is extinct. In reality, however, the task is much more complex. Techniques such as optimal linear estimation, in combination with other data sources, and knowledge of recording effort, may prove useful in inferring extinction across a variety of taxa but should not be used in isolation.     

Acipenser sturio and Acipenser nudiventris in the Danube – extant or extinct?

The presence of Atlantic sturgeon ( Acipenser sturio) and ship sturgeon ( Acipenser nudiventris ) in the Danube has been known through only occasional, chance sightings; significant uncertainty remains as to whether these species are already extinct or still present in the Danube River basin. In this study, five different statistical methods were applied for assessment of their extinction probability. All methods provided a significant probability that the Atlantic sturgeon is extinct, with extinction having occurred somewhere between 1966 and 1970. Although the applied methods provided different results, all indicated that the ship sturgeon is probably still present, but that extinction may occur within a few decades. Sensitivity analyses of these statistical methods projected that new sightings of ship sturgeon in the coming years would not extend the length of extinction by more than a few years. The best management approach for these two species, given the lack of knowledge on their presence in the Danube River basin, could be to apply all feasible protection measures for the other four Danube sturgeon species. These measures could at the same time provide protection for these two species, presuming they are not already extinct or beyond recovery.     

Herbarium records do not predict rediscovery of presumed nationally extinct species

Rediscoveries of species previously thought to be extinct present a dilemma to conservation biology. On one hand, such instances offer the chance to change the course of events away from one that would have led to extinctions. On the other hand, public support for conservation may wane if scientists are frequently seen to overstate and prematurely declare extinctions. Recent studies have adopted a probabilistic approach to infer extinction, using sightings or collections and statistical models to calculate the chance that a species may still be extant. We conduct the first broad-scale test of such models using a recently compiled national red list and national herbarium collection records, including collections of presumed nationally extinct species made after the red list publication, which constitute “rediscoveries”. There was little evidence that the probabilities calculated by these models were associated with rediscoveries over a 3.5-year period. Current probabilistic models of extinction using sighting records could hence be inadequate for use with most natural history collection data.     

Accounting for observation reliability when inferring extinction based on sighting records

Given the current increase in global extinction risk of species, methods that are able to estimate the probability and the time of extinction based on a sighting record of a rare or poorly studied species are becoming increasingly important. One of the major obstacles when using such methods is that many sighting records are burdened with uncertain or controversial observations. What is accepted as a valid sighting can have a substantial effect on resulting predictions. Here we present a simple modification to an existing method that allows for the inclusion of specific sighting reliabilities of individual observations into predictions of the likelihood and the time of extinction. The approach is applied to the sighting records of four presumably extinct bird species. Results indicated that the Ivory-billed Woodpecker (Campephilus principalis) and the Eskimo Curlew (Numenius borealis) may be considered as extinct, even when recent controversial sightings are included in the analysis. The Nukupu`u (Hemignathus lucidus) and O`ahu `Alauahio (Paroreomyza maculata) could potentially still be extant, although with a low probability of persistence. The major advantage of the presented method is that, instead of applying some arbitrary threshold for the sighting reliability that is considered acceptable, it recognizes and incorporates the reliability of each observation into the resulting predictions, by estimating the most likely number of observations and the most likely time of the last observation. Its simplicity facilitates its application for assessments of a larger number species or populations, and makes it accessible as a decision tool.     

Correlations in fossil extinction and origination rates through geological time

Recent analyses have suggested that extinction and origination rates exhibit long-range correlations, implying that the fossil record may be controlled by self-organized criticality or other scale-free internal dynamics of the biosphere. Here we directly test for correlations in the fossil record by calculating the autocorrelation of extinction [corrected] and origination rates through time. Our results show that extinction rates are uncorrelated beyond the average duration of a stratigraphic interval. Thus, they lack the long-range correlations predicted by the self-organized criticality hypothesis. In contrast, origination rates show strong autocorrelations due to long-term trends. After detrending, origination rates generally show weak positive correlations at lags of 5-10 million years (Myr) and weak negative correlations at lags of 10-30 Myr, consistent with aperiodic oscillations around their long-term trends. We hypothesize that origination rates are more correlated than extinction rates because originations of new taxa create new ecological niches and new evolutionary pathways for reaching them, thus creating conditions that favour further diversification.     

Examining the Extinction of the Barbary Lion and Its Implications for Felid Conservation

Estimations of species extinction dates are rarely definitive, yet declarations of extinction or extirpation are important as they define when conservation efforts may cease. Erroneous declarations of extinctions not only destabilize conservation efforts but also corrode local community support. Mismatches in perceptions by the scientific and local communities risk undermining sensitive, but important partnerships. We examine observations relating to the decline and extinction of Barbary lions in North Africa. Whilst the extinction predates the era of the scientific conservation movement, the decline is relatively well documented in historical records. Recently unearthed accounts suggest Barbary lions survived later than previously assumed. We use probabilistic methods to estimate a more recent extinction date for the subspecies. The evidence presented for a much later persistence of lions in North Africa, including generations when sightings were nil, suggests caution when considering felid populations as extinct in the wild. The case raises the possibility that captive animals descended from the Moroccan royal collection are closer contemporaries to wild Barbary lions. Furthermore, our results highlight the vulnerability of very small lion populations and the significance of continued conservation of remnant lion populations in Central and West Africa.     

Assessing the role of off‐take and source–sink dynamics in the extinction of the amphidromous New Zealand grayling (Prototroctes oxyrhynchus)

相似文献   

Uncertainty in identifying local extinctions: the distribution of missing data and its effects on biodiversity measures

Identifying local extinctions is integral to estimating species richness and geographic range changes and informing extinction risk assessments. However, the species occurrence records underpinning these estimates are frequently compromised by a lack of recorded species absences making it impossible to distinguish between local extinction and lack of survey effort—for a rigorously compiled database of European and Asian Galliformes, approximately 40% of half-degree cells contain records from before but not after 1980. We investigate the distribution of these cells, finding differences between the Palaearctic (forests, low mean human influence index (HII), outside protected areas (PAs)) and Indo-Malaya (grassland, high mean HII, outside PAs). Such cells also occur more in less peaceful countries. We show that different interpretations of these cells can lead to large over/under-estimations of species richness and extent of occurrences, potentially misleading prioritization and extinction risk assessment schemes. To avoid mistakes, local extinctions inferred from sightings records need to account for the history of survey effort in a locality.     

Extinction of South American sparassodontans (Metatheria): environmental fluctuations or complex ecological processes?

Sparassodontans are a diverse but now extinct group of metatherians that were apex predators in South America during most of the Cenozoic. Studying their decline has been controversial mainly due to the scarcity of the fossil record, and different methodological approaches have led to contradictory hypotheses. In an effort to explore questions about their extinction, we developed a novel multi‐model statistical approach to analyse all of the currently available data at a continental scale. Using multiple regression analysis and new advances in beta diversity analysis, we used all currently available fossil data at a continental scale to test four competing hypotheses to account for the decline of sparassodontans: competition with placental carnivorans, competition with avian phorusrhacids, non‐competitive ecological interactions, and environmental fluctuations. Our results show that the sparassodontan extinction was a gradual process with species disappearing throughout the Cenozoic. Multiple regression analysis supported non‐competitive ecological interactions as the best extinction model. Native South American ungulates, African migrants (caviomorph rodents and platyrrhine primates) and didelphimorphians were the groups with the highest statistical significance. Sparassodontan beta diversity increased between South American Land Mammal Ages after the Paleocene–Eocene boundary. Our results demonstrate that ecological modelling techniques illuminate aspects of extinction processes whilst mitigating the limitations of the fossil record. Our study suggests that non‐competitive ecological interactions could have been the main driver for sparassodontan extinction rather than, as commonly assumed, a result of competition and/or abiotic fluctuations.     

Recognizing pulses of extinction from clusters of last occurrences

The distribution of last occurrences of fossil taxa in a stratigraphic column are used to infer the pattern, timing and tempo of extinction from the fossil record. Clusters of last occurrences are commonly interpreted as an abrupt pulse of extinction. However, stratigraphic architecture alone can produce clusters of last occurrences that can be misinterpreted as an extinction pulse. These clusters will typically occur in strata that immediately underlie facies changes and sequence‐stratigraphic surfaces. It has been proposed that a basin‐wide analysis of the fossil record within a sequence‐stratigraphic framework can be used to distinguish between clusters of last occurrences caused solely by extinction pulses from those generated by sequence‐stratigraphic architecture. A basin‐wide approach makes it possible to observe lateral facies shifts in response to sea‐level change, mitigating the effects of stratigraphic architecture. Using computer simulations of plausible Late Ordovician mass‐extinction scenarios tuned to an inferred Late Ordovician sea‐level curve, we show that stratigraphically‐generated clusters of last occurrences are observed even in basin‐wide analyses of the simulated fossil records due to the basin‐wide loss of preferred facies for many taxa. Nonetheless, we demonstrate that by coarsening the stratigraphic resolution to the systems‐tract level and identifying facies preferences of simulated taxa, we can filter out taxa whose last occurrences coincide with the basin‐wide loss of their preferred facies. This enables consistent identification of the underlying extinction pattern for a wide variety of extinction scenarios. Applying this approach to empirical field data can help to constrain underlying extinction patterns from the fossil record.     

Evaluating the predicted extinction risk of living amphibian species with the fossil record

Bridging the gap between the fossil record and conservation biology has recently become of great interest. The enormous number of documented extinctions across different taxa can provide insights into the extinction risk of living species. However, few studies have explored this connection. We used generalised boosted modelling to analyse the impact of several traits that are assumed to influence extinction risk on the stratigraphic duration of amphibian species in the fossil record. We used this fossil‐calibrated model to predict the extinction risk for living species. We observed a high consensus between our predicted species durations and the current IUCN Red List status of living amphibian species. We also found that today's Data Deficient species are mainly predicted to experience short durations, hinting at their likely high threat status. Our study suggests that the fossil record can be a suitable tool for the evaluation of current taxa‐specific Red Listing status.     

The mid-Holocene extinction of silver fir (Abies alba) in the Southern Alps: a consequence of forest fires? Palaeobotanical records and forest simulations

Pollen records suggest that Abies alba played a dominating role in both the montane and lowland forests at the border of the Southern Alps between ca. 8500 and 5700 years ago. Two major declines in fir, at about 7300–7000 cal b.p. and at ca. 6000 cal b.p., followed by the local extinction of the species are characteristic of the area below ca. 1000 m a.s.l. In order to test the impact of fire on the population dynamics of silver fir, a dynamic model (DisCForm) with a fire module was applied to simulate the early- and mid-Holocene forest development. Simulation outputs based on different fire scenarios were compared with the pollen record from Lago di Annone (226 m a.s.l.). The marked Abies decreases shown in the pollen record can be simulated with very intensive fire scenarios, but they do not result in an extinction of silver fir in the model. Low charcoal influx values related to the Abies declines in the palaeobotanical record suggest that fire was not the only reason for the extinction of silver fir. Human impact, as well as Holocene climatic changes leading to temporary moisture deficits and reduced adaptability due to low genetic variation may have had a significant impact on the Abies forests.     

How to infer population trends in sparse data: examples with opportunistic sighting records for great white sharks

Aim Biodiversity is declining at accelerating rates. Understanding past and ongoing changes to biodiversity is paramount in prioritizing conservation action and restoring functional ecosystems. Yet long‐term, systematic data on the distribution and abundance of species are sparse. For many organisms, specimen collections and anecdotal accounts of chance sightings or captures constitute the only source of information. Such data have the potential to provide valuable insights on long‐term ecosystem changes, but are often neglected because they are difficult to analyse quantitatively. Here we review available methods and introduce a new approach. Location Historic data on sightings and captures of great white sharks in the eastern Adriatic and off eastern Canada serve to illustrate the utility of both the existing methods and the new approach. Method Unlike existing methods, the new approach focuses on estimating population trends rather than verifying extinction and explicitly addresses uncertainty over observation effort via two tiers of sensitivity analysis. It fits a series of generalized linear models that provide multiple estimates of declines under alternate scenarios regarding the appropriate reference period and observer trends. Programming code to implement the approach in freely available software is provided as supplementary material. Results Example analyses of great white shark sightings suggest that local populations of this species have suffered dramatic declines, both in the eastern Adriatic and along Canada’s eastern coast. Although not yet extinct, this top predator may therefore no longer be able to fulfil its former ecological role. Main conclusions Careful quantitative analyses of imperfect historical data can provide valuable insights into past ecological changes. Such insights are crucial to improved management and restoration of individual species and their ecosystems. We therefore hope that our review of available methods will facilitate quantitative evaluations of species for which analysis was previously impeded by a lack of systematically collected data.     

Interactions within and between clades shaped the diversification of terrestrial carnivores

A longstanding debate in evolutionary biology and paleontology is whether ecological interactions such as competition impose diversity dependence on speciation and extinction rates. Here, we analyze the fossil record of terrestrial mammalian carnivores in North America and Eurasia using a Bayesian framework to assess whether their diversity dynamics were affected by diversity dependence within and between families (12 in Eurasia, 10 in North America). We found eight instances of within‐clade diversity dependence suppressing speciation rates and detected between‐clade effects increasing extinction rates in six instances. Diversity dependence often involved lineages that migrated between continents and we found that speciation was more responsive to diversity changes within the clade, whereas extinction responded to diversity of taxa in other clades. The analysis of the fossil record of Carnivora suggests that interactions within and between clades are associated with different speciation and extinction regimes, opening room for a broader theory of diversity dependence.     

Mass extinction events and the plant fossil record

Five mass extinction events have punctuated the geological record of marine invertebrate life. They are characterized by faunal extinction rates and magnitudes that far exceed those observed elsewhere in the geological record. Despite compelling evidence that these extinction events were probably driven by dramatic global environmental change, they were originally thought to have little macroecological or evolutionary consequence for terrestrial plants. New high-resolution regional palaeoecological studies are beginning to challenge this orthodoxy, providing evidence for extensive ecological upheaval, high species-level turnover and recovery intervals lasting millions of years. The challenge ahead is to establish the geographical extent of the ecological upheaval, because reconstructing the vegetation dynamics associated with these events will elucidate the role of floral change in faunal mass extinction and provide a better understanding of how plants have historically responded to global environmental change similar to that anticipated for our future.     

EXTINCTION DURING EVOLUTIONARY RADIATIONS: RECONCILING THE FOSSIL RECORD WITH MOLECULAR PHYLOGENIES

Recent application of time‐varying birth–death models to molecular phylogenies suggests that a decreasing diversification rate can only be observed if there was a decreasing speciation rate coupled with extremely low or no extinction. However, from a paleontological perspective, zero extinction rates during evolutionary radiations seem unlikely. Here, with a more comprehensive set of computer simulations, we show that substantial extinction can occur without erasing the signal of decreasing diversification rate in a molecular phylogeny. We also find, in agreement with the previous work, that a decrease in diversification rate cannot be observed in a molecular phylogeny with an increasing extinction rate alone. Further, we find that the ability to observe decreasing diversification rates in molecular phylogenies is controlled (in part) by the ratio of the initial speciation rate (Lambda) to the extinction rate (Mu) at equilibrium (the LiMe ratio), and not by their absolute values. Here we show in principle, how estimates of initial speciation rates may be calculated using both the fossil record and the shape of lineage through time plots derived from molecular phylogenies. This is important because the fossil record provides more reliable estimates of equilibrium extinction rates than initial speciation rates.     

Courtship and mating behaviour of manta rays Mobula alfredi and M. birostris in the Maldives

The aim of this 14 year study was to elucidate the entire courtship and mating behaviour of manta rays Mobula alfredi and M. birostris using behavioural observations, video and photographic records. From 2003 to 2016, over 11,000 surveys were undertaken at known manta ray aggregation sites in the Maldives to record any observed manta rays reproductive activity. From 47,591 photo‐ID sightings, 4,247 individual M. alfredi were identified and 226 individual M. birostris from 229 photo‐ID sightings, all recorded at 22 atolls across 265 different sites. Courtship activity was observed on 206 surveys at 30 different sites. A total of 229 courtship events were recorded, with 90% (n = 205) of them occurring at cleaning sites. The observed courtship activity was categorised into seven distinct stages which are described in detail: initiation, endurance, evasion, pre‐copulatory positioning, copulation, post‐copulatory holding and separation. Photographs provide the first scientific record of the entirety of manta rays courtship and mating. Both M. alfredi and M. birostris appear to engage in the same elaborate courtship rituals, exhibiting the same behaviours during all stages of the courtship and mating process.     

Killer whale predation on subantarctic fur seals at Prince Edward Island, Southern Indian Ocean

Killer whales at subantarctic Marion Island have been subjected to several scientific studies. In contrast, up until recently, there has been only one record of these animals documented for neighbouring Prince Edward Island. We here report on killer whale observations at Prince Edward Island during March 2012. During 3?days of opportunistic observations at a fur seal colony on the island, killer whales were sighted on six occasions. These probably represented three different pods numbering 11 individuals in total. During all sightings, individuals were seen hunting subantarctic fur seal pups, with four successful predatory events observed.     

Hunt sightings as a tool for monitoring the distribution and abundance of brown hare <Emphasis Type="Italic">Lepus europaeus</Emphasis> in UK agricultural landscapes

We examined the potential of hare sightings data, collected during hunts by the Association of Masters of Harriers and Beagles, as a possible monitoring tool for the European brown hare Lepus europaeus. The relationship between land use and both temporal trends, and spatial patterns, in brown hare sightings across England and Wales was examined using data collected between the 1985/86 and 2004/05 hunting seasons. Hare sightings increased significantly during this period, with an average increase of 2.81 hare sightings per hunting day across all hunts since 1985. Sightings were more frequent in eastern England, where arable land is abundant, than in the rest of England and Wales which is predominantly pastoral. There was no correlation between temporal trends in hare sightings and land use change. Patterns observed using the hunt sighting data are similar to those reported by other concurrent studies that used different methods. We conclude that hunt sightings could contribute useful data to a national monitoring scheme.