Extinction Date Research Articles

Assembling an illustrated family‐level tree of life for exploration in mobile devices

AbstractSince the concept of the tree of life was introduced about 150 years ago, a considerable fraction of the scientific community has focused its efforts on its reconstruction, with remarkable progress during the last two decades with the advent of DNA sequences. However, the assemblage of a comprehensive and explorable tree of life has been a difficult task to achieve due to two main obstacles: (i) information is scattered into several individual sources and (ii) practical visualization tools for exploring large trees are needed. To overcome both challenges, we aimed to synthesize a family‐level tree of life by compiling over 1400 published phylogenetic studies, choosing the source trees that represent the best phylogenetic hypotheses to date based on a set of objective criteria. Moreover, we dated the tree by employing over 550 secondary calibrations using publicly available sequences for more than 5000 taxa and by incorporating age ranges from the fossil record for over 2800 taxa. Additionally, we developed a mobile app for smartphones to facilitate the visualization and exploration of the resulting tree. Interactive features include exploration by the zooming and panning gestures of touch screens, collapsing branches, visualizing specific clades as subtrees, a search engine, and a timescale to determine extinction and divergence dates, among others. Small illustrations of organisms are displayed at the terminals to better visualize the morphological diversity of life. Our assembled tree currently includes over 7000 families, and its content will be expanded through regular updates to cover all life on earth at the family level.

Did Captain Beechey see a living Mandarina luhuana, an extinct land snail species?

ABSTRACT Knowledge about prehuman biotas and the impact of early human contact, particularly on land snails inhabiting oceanic islands, is still poor. One specific example of interest is Mandarina luhuana, which was first collected from the Chichijima Islands of the Ogasawara Archipelago in 1827 during Captain Frederick William Beechey's expedition. The initial description of M. luhuana included an image of a shell with dark brown pigmentation, which contrasts with current understanding, with all known specimens being considered to lack dark colouration. Traditionally, it is believed that M. luhuana represents a fossil species that became extinct on the island before human arrival. However, I propose that the specimen collected for the original description was either recently dead or still alive at the time of collection. Furthermore, I hypothesize that M. luhuana faced extinction after human arrival on Ogasawara, which began during the 17th century. To test this hypothesis, I used accelerator mass spectrometry dating to determine the extinction dates of subfossil samples of M. luhuana. The results of this study suggest that M. luhuana became extinct after the 17th century, with the species having possibly survived until the early 19th century. It is likely that the extinction of M. luhuana occurred shortly after human arrival in the islands. These findings underscore the need for further research to understand the impact of human arrival on island ecosystems and to uncover the original diversity of land snail faunas on islands.

Resolving when (and where) the Thylacine went extinct

Like the Dodo and Passenger Pigeon before it, the predatory marsupial Thylacine (Thylacinus cynocephalus), or ‘Tasmanian tiger’, has become an iconic symbol of anthropogenic extinction. The last captive animal died in 1936, but even today reports of the Thylacine's possible ongoing survival in remote regions of Tasmania are newsworthy and capture the public's imagination. Extirpated from mainland Australia in the mid-Holocene, the island of Tasmania became the species' final stronghold. Following European settlement in the 1800s, the Thylacine was relentlessly persecuted and pushed to the margins of its range, although many sightings were reported thereafter—even well beyond the 1930s. To gain a new depth of insight into the extinction of the Thylacine, we assembled an exhaustive database of 1237 observational records from Tasmania (from 1910 onwards), quantified their uncertainty, and charted the patterns these revealed. We also developed a new method to visualize the species' 20th-century spatio-temporal dynamics, to map potential post-bounty refugia and pinpoint the most-likely location of the final persisting subpopulation. A direct reading of the high-quality records (confirmed kills and captures, in combination with sightings by past Thylacine hunters and trappers, wildlife professionals and experienced bushmen) implies a most-likely extinction date within four decades following the last capture (i.e., 1940s to 1970s). However, uncertainty modelling of the entire sighting record, where each observation is assigned a probability and the whole dataset is then subject to a sensitivity analysis, suggests that extinction might have been as recent as the late 1980s to early 2000s, with a small chance of persistence in the remote south-western wilderness areas. Beyond the intrinsically fascinating problem of reconstructing the final fate of the Thylacine, the new spatio-temporal mapping of extirpation developed herein would also be useful for conservation prioritization and search efforts for other rare taxa of uncertain status.

Characteristics of Heat Waves in Mainland China since 1961 Based on Absolute and Relative Methods

Based on gridded temperature data from the China Meteorological Administration (CMA), two types of methods, i.e., absolute methods and relative methods, respectively, were used to identify heat waves in Mainland China. Four statistical indicators, including the occurrence frequency, duration days, earliest occurrence date, and latest extinction date, were constructed to analyze the spatial-temporal characteristics of heat waves, especially on the annual and decadal change trends. Firstly, we found that both the frequency and the duration of heat waves decreased in the period from 1960 to 1989 but increased in the 1990s and increased significantly from the early 2000s to the 2010s. Spatially, the frequency and the duration obtained by each type of method are significantly different among different regions when considering different facts, such as different regions that have different degrees of tolerance to heat waves. Secondly, the decadal distribution characteristics of the earliest occurrence date and the latest extinction date of heat waves well capture the hot summer, the stronger sensitivity of winter to warming than other seasons, and the gradually increasing intensity of heat waves. It provides a multidimensional reference for the cause analysis and prediction of extreme heat waves in China.

Challenges for incorporating long‐term baselines into biodiversity restoration: A case study of the Dalmatian Pelican (Pelecanus crispus) in Britain

Species reintroductions are a core component of conservation but require critical assessment of past baselines. The Dalmatian Pelican Pelecanus crispus formerly occurred in Britain during the Holocene and there is interest in its possible reintroduction, but its regional extinction dynamics remain poorly understood. Pelican bones are known from subfossil and zooarchaeological contexts at 11 British Holocene sites in three regions (East Anglian Fens, Somerset Levels and Moors, Humber Valley). Dalmatian Pelican is positively identified from four of these sites, with other specimens only identified to genus level. Pelican populations were probably only present periodically in Britain during intervals of suitable climate and available habitat: there is little evidence for pelicans before the Bronze Age, and most sites are known or inferred to be Iron Age. There is a suggested Medieval specimen but no secure evidence of pelican presence after the Roman period. However, no specimens are directly dated, with age estimation reliant upon indirect dates or inference. Climatic niche modelling indicates that southern Britain was the northwestern limit of pelican climate tolerance under postglacial conditions, and pelicans may have been unable to persist regionally until the mid‐ or late Holocene. Considerable pelican breeding and foraging habitat might have existed until the Medieval period, but availability of suitable habitat fluctuated throughout the Holocene. Probabilistic analysis suggests possible mean extinction date estimates between ad 589 and ad 1587, highlighting uncertainty associated with indirect data, and hindering our ability to correlate pelican disappearance with putative extinction drivers (overexploitation, human modification of wetlands, or non‐anthropogenic environmental changes). Improving our understanding of conditions associated with past pelican occurrence is essential for potential reintroduction decision‐making, and direct dating of bones from all sites is needed to establish a secure chronological framework for correlating pelican presence and disappearance with regional landscape change. This review provides a robust framework for how to integrate past environmental baselines into conservation decision‐making and reintroduction feasibility assessments.

Optimal linear estimation models predict 1400–2900 years of overlap between Homo sapiens and Neandertals prior to their disappearance from France and northern Spain

Recent fossil discoveries suggest that Neandertals and Homo sapiens may have co-existed in Europe for as long as 5 to 6000 years. Yet, evidence for their contemporaneity at any regional scale remains highly elusive. In France and northern Spain, a region which features some of the latest directly-dated Neandertals in Europe, Protoaurignacian assemblages attributed to Homo sapiens appear to ‘replace’ Neandertal-associated Châtelperronian assemblages. Using the earliest and latest known occurrences as starting points, Bayesian modelling has provided indication that these occupations may in fact have been partly contemporaneous. The reality, however, is that we are unlikely to ever identify the ‘first’ or ‘last’ appearance of a species or cultural tradition in the archaeological and fossil record. Here, we use optimal linear estimation modelling to estimate the first appearance date of Homo sapiens and the extinction date of Neandertals in France and northern Spain by statistically inferring these ‘missing’ portions of the Protoaurignacian and Châtelperronian archaeological records. Additionally, we estimate the extinction date of Neandertals in this region using a dataset of directly-dated Neandertal fossil remains. Our total dataset consists of sixty-six modernly produced radiocarbon determinations which we recalibrated using the newest calibration curve (IntCal20) to produce updated age ranges. The results suggest that the onset of the Homo sapiens occupation of this region likely preceded the extinction of Neandertals and the Châtelperronian by up to 1400–2900 years. This reaffirms the Bayesian-derived duration of co-existence between these groups during the initial Upper Palaeolithic of this region using a novel independent method, and indicates that our understanding of the timing of these occupations may not be suffering from substantial gaps in the record. Whether or not this co-existence featured some form of direct interaction, however, remains to be resolved.

Outbreaks of COVID-19 in indoor places of worship: a systematic review.

This review aimed to describe what has been published on COVID-19 outbreaks originating from indoor places of worship. A systematic review was conducted following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) checklist by searching PubMed, Scopus and Embase from 1 January 2020 to 29 March 2021. Citation chasing was also performed. Studies with information about COVID-19 outbreaks originating in indoor places of worship of any religion were included. A total of 9729 records were identified and 36 were selected. The articles reported 119 descriptions of outbreaks linked to churches, mosques, synagogues, and temples, referring to approximately 52-74 unique outbreaks. The outbreaks were mostly located in three major areas: East and Southeast Asia (46%), the USA (27%), Europe (22%). All the outbreaks began in 2020. Mainly, there were no restrictive measures, or such measures were not followed at the time of the outbreak. Choir practices presented the highest attack rate (up to 0.867). The lack of preventive measures and the role of singing practices were highlighted. Reports were often lacking contact tracing and sometimes did not report the date of outbreak extinction. Moreover, reports came from few geographical areas. Thus, the impact of transmission in places of worship may be largely underestimated.

Ancient proteins resolve controversy over the identity of Genyornis eggshell

The realization that ancient biomolecules are preserved in "fossil" samples has revolutionized archaeological science. Protein sequences survive longer than DNA, but their phylogenetic resolution is inferior; therefore, careful assessment of the research questions is required. Here, we show the potential of ancient proteins preserved in Pleistocene eggshell in addressing a longstanding controversy in human and animal evolution: the identity of the extinct bird that laid large eggs which were exploited by Australia's indigenous people. The eggs had been originally attributed to the iconic extinct flightless bird Genyornis newtoni (†Dromornithidae, Galloanseres) and were subsequently dated to before 50 ± 5 ka by Miller etal. [Nat. Commun. 7, 10496 (2016)]. This was taken to represent the likely extinction date for this endemic megafaunal species and thus implied a role of humans in its demise. A contrasting hypothesis, according to which the eggs were laid by a large mound-builder megapode (Megapodiidae, Galliformes), would therefore acquit humans of their responsibility in the extinction of Genyornis. Ancient protein sequences were reconstructed and used to assess the evolutionary proximity of the undetermined eggshell to extant birds, rejecting the megapode hypothesis. Authentic ancient DNA could not be confirmed from these highly degraded samples, but morphometric data also support the attribution of the eggshell to Genyornis. When used in triangulation to address well-defined hypotheses, paleoproteomics is a powerful tool for reconstructing the evolutionary history in ancient samples. In addition to the clarification of phylogenetic placement, these data provide a more nuanced understanding of the modes of interactions between humans and their environment.

The role of habitat fragmentation in Pleistocene megafauna extinction in Eurasia

The idea that several small, rather than a single large, habitat areas should hold the highest total species richness (the so‐called SLOSS debate) brings into question the importance of habitat fragmentation to extinction risk. SLOSS studies are generally addressed over a short time scale, potentially ignoring the long‐term dimension of extinction risk. Here, we provide the first long‐term evaluation of the role of habitat fragmentation in species extinction, focusing on 22 large mammal species that lived in Eurasia during the last 200 000 years. By combining species distribution models and landscape pattern analysis, we compared temporal dynamics of habitat spatial structure between extinct and extant species, estimating the size, number and degree of the geographical isolation of their suitable habitat patches. Our results evidenced that extinct mammals went through considerable habitat fragmentation during the last glacial period and started to fare worse than extant species from about 50 ka. In particular, our modelling effort constrains the fragmentation of habitats into a narrow time window, from 46 to 36 ka ago, surprisingly coinciding with known extinction dates of several megafauna species. Landscape spatial structure was the second most important driver affecting megafauna extinction risk (ca 38% importance), after body mass (ca 39%) and followed by dietary preferences (ca 20%). Our results indicate a major role played by landscape fragmentation on extinction. Such evidence provides insights on what might likely happen in the future, with climate change, habitat loss and fragmentation acting as the main forces exerting their negative effects on biodiversity.

The importance of model assumptions in estimating the dynamics of the COVID-19 epidemic

Estimating the date at which an epidemic started in a country and the date at which it can end depending on interventions intensity are important to guide public health responses. Both are potentially shaped by similar factors including stochasticity (due to small population sizes), superspreading events, and ‘memory effects’ (the fact that the occurrence of some events, e.g. recovering from an infection, depend on the past, e.g. the number of days since the infection). Focusing on COVID-19 epidemics, we develop and analyse mathematical models to explore how these three factors may affect early and final epidemic dynamics. Regarding the date of origin, we find limited effects on the mean estimates, but strong effects on their variances. Regarding the date of extinction following lockdown onset, mean values decrease with stochasticity or with the presence of superspreading events. These results underline the importance of accounting for heterogeneity in infection history and transmission patterns to accurately capture early and late epidemic dynamics.

The two extinctions of the Carolina ParakeetConuropsis carolinensis

SummaryDue to climate change and habitat conversion, estimates of the resulting levels of species extinction over the next century are alarming. Devising conservation solutions will require many different approaches, including examining the extinction processes of recently extinct species. Given that parrots are one of the most threatened groups of birds, information regarding parrot extinction is pressing. While most recent parrot extinctions have been island endemics, the Carolina ParakeetConuropsis carolinensishad an 18th-century range covering nearly half of the present-day United States, yet mostly disappeared by the end of the 19thcentury. Despite a great deal of speculation, the major cause of its extinction remains unknown. Establishing the date when a species went extinct is one of the first steps in determining what caused their extinction. While there have been estimates of their extinction date, these analyses used a limited dataset and did not include observational data. We used a recently published, extensive dataset of Carolina Parakeet specimens and observations combined with a Bayesian extinction estimating model to determine the most likely extinction dates. By considering each of the two subspecies independently, we found that they went extinct ˜30 years apart: the western subspeciesC. c. ludovicianusgoing extinct around 1914 and the eastern subspeciesC. c. carolinensiseither in the late 1930s or mid-1940s. Had we only considered all observations together, this pattern would have been obscured, possibly missing a major clue in solving the mystery of the parakeet’s extinction. Since the Carolina Parakeet was a wide-ranging species that went extinct during a period of rapid agricultural and industrial expansion, conditions that mirror those occurring in many parts of the world where parrot diversity is highest, any progress we make in unraveling the mystery of their disappearance may be vital to modern conservation efforts.

Simultaneous extinction of Madagascar's megaherbivores correlates with late Holocene human-caused landscape transformation

Reconstructing the dynamics and drivers of late Quaternary megafaunal extinctions requires direct radiometric date series that are assessed within probabilistic statistical frameworks. Extinction chronologies are poorly understood for many tropical regions, including Madagascar, which had a diverse, now-extinct Holocene large vertebrate fauna including a “megaherbivore” guild of endemic hippopotami and elephant birds. Madagascar's megaherbivores likely played vital roles in regulating ecosystem structure and nutrient cycling, but few direct dates are available for megaherbivore specimens identified to species level, with uncertainty over when and why different representatives of this guild disappeared. Here, we conduct a new investigation into Malagasy megaherbivore extinction dynamics, including 30 new AMS dates and 63 audited published dates. We use Gaussian-resampled inverse-weighted McInerny (GRIWM) analysis to estimate species-specific extinction dates for three elephant bird species (Aepyornis hildebrandti, Mullerornis modestus, Vorombe titan), eggshell representing Aepyornis or Vorombe, and two hippo species (Hippopotamus lemerlei, H. madagascariensis), and to estimate extinction dates for megaherbivore communities in different biomes. Megaherbivores persisted for millennia after first human arrival. Extinction date estimates vary significantly between biomes, with disappearance from dry deciduous forest over a millennium earlier than other biomes, possibly reflecting local variation in megaherbivore population densities or human pressures. However, megaherbivore communities including all elephant bird and hippo species persisted elsewhere across Madagascar until ∼1200-900 bp, when they collapsed suddenly. Extinctions are closely correlated in time with intensive conversion of forests to grassland at ∼1100-1000 bp, probably associated with a shift to agro-pastoralism and representing a radical change in sustainability of prehistoric human interactions with biodiversity.

Modelling the end of the Acheulean at global and continental levels suggests widespread persistence into the Middle Palaeolithic

The Acheulean is the longest cultural tradition ever practised by humans, lasting for over 1.5 million years. Yet, its end has never been accurately dated; only broad 300–150 thousand years ago (Kya) estimates exist. Here we use optimal linear estimation modelling to infer the extinction dates of the Acheulean at global and continental levels. In Africa and the Near East the Acheulean is demonstrated to end between 174 and 166 Kya. In Europe it is inferred to end between 141 and 130 Kya. The Acheulean’s extinction in Asia occurs later (57–53 Kya), while global models vary depending on how archaeological sites are selected (107–29 Kya). These models demonstrate the Acheulean to have remained a distinct cultural tradition long after the inception of Middle Palaeolithic technologies in multiple continental regions. The complexity of this scenario mirrors the increasingly dynamic nature of the Middle Pleistocene hominin fossil record, suggesting contemporaneous hominin populations to have practised distinct stone-tool traditions.

Genetic barcoding of museum eggshell improves data integrity of avian biological collections

Natural history collections are often plagued by missing or inaccurate metadata for collection items, particularly for specimens that are difficult to verify or rare. Avian eggshell in particular can be challenging to identify due to extensive morphological ambiguity among taxa. Species identifications can be improved using DNA extracted from museum eggshell; however, the suitability of current methods for use on small museum eggshell specimens has not been rigorously tested, hindering uptake. In this study, we compare three sampling methodologies to genetically identify 45 data-poor eggshell specimens, including a putatively extinct bird’s egg. Using an optimised drilling technique to retrieve eggshell powder, we demonstrate that sufficient DNA for molecular identification can be obtained from even the tiniest eggshells without significant alteration to the specimen’s appearance or integrity. This method proved superior to swabbing the external surface or sampling the interior; however, we also show that these methods can be viable alternatives. We then applied our drilling method to confirm that a purported clutch of Paradise Parrot eggs collected 40 years after the species’ accepted extinction date were falsely identified, laying to rest a 53-year-old ornithological controversy. Thus, even the smallest museum eggshells can offer new insights into old questions.

Inferring extinction date of a species using non‐homogeneous Poisson processes with a change‐point

Abstract Bayesian methods have been developed for inferring the true year of extinction of a species from sighting records that have both certain and uncertain sightings. These methods typically make the restrictive assumption that all sighting types (i.e. certain, valid uncertain, invalid uncertain) derive from constant rate Poisson processes. In this study, the constant rate assumption in the homogeneous Poisson process is relaxed by allowing certain and uncertain sightings to follow independent non‐homogeneous Poisson processes. The model can thus identify whether any of the sighting rates were increasing, decreasing or constant. In addition, a change‐point is introduced to model the uncertain sightings, where the sighting rates before and after the change‐point vary. We have used Markov Chain Monte Carlo (MCMC) sampling to generate the posterior distributions for model parameters including species extinction time. The proposed method was applied to the sighting records of the black‐footed ferret Mustela nigripes and the ivory‐billed woodpecker Campephilus principalis (IBW) species. Based on a hypothesis test, the results of the model indicate that the species both went extinct in the years 1988 and 1956 respectively. Moreover, a decline in the certain sighting rate was also inferred for both these species, possibly indicating the decrease in the species abundance as it converges to extinction. Thus, earlier models that assume a constant sighting rate may well be biased. Uncertain sighting rates for the IBW were found to increase before extinction (indicating possibly some additional ecological attention received near extinction) and remained constant after extinction.

On the possible vernacular name and origin of the extinct Spotted Green Pigeon Caloenas maculata

I reviewed data from historical works and a dictionary produced by the first missionaries in French Polynesia, in an endeavour to clarify the geographic provenance and potential date of extinction of the bird known as tītī in Tahiti, and which has been assumed to be the extinct Spotted Green Pigeon Caloenas maculata, otherwise known from a single surviving specimen held in Liverpool (UK). The name tītī was used to refer to a columbid, as well as to procellariids, and to other species whose vocalisations are transcribed ti-ti-ti. Furthermore, what was presumably the same species was also known as the tītīhope'ore, which according to the Tahitian people resembled a Long-tailed Koel Urodynamis taitensis but had a short tail. Spotted Green Pigeon possibly survived until sometime between 1801 and 1831, but by 1848 the species was almost certainly extinct, making the claim that it was seen in Tahiti as late as 1928 appear exceptionally unlikely.

Is the New England medicinal leech (Macrobdella sestertia) extinct?

Despite recent interest in invertebrate extinctions, most go undocumented due to chronic data deficiencies. Here, we investigate the absence of the New England medicinal leech (Macrobdella sestertia), a species not sighted in the last decade, but which has been rediscovered several times since it was described in 1886. We collate all known records (19 specimens from nine independent sightings) of this rare species, and use sighting-based extinction date estimators to evaluate the odds that populations of M. sestertia might persist. Using all available data and several different models, we find that while the species may be extinct, there is also not enough evidence to eliminate the hypothesis that the species remains extant. Given that the geographic range of M. sestertia is now known to extend much further south than previously thought, we recommend protections for M. sestertia should be expanded at state and potentially federal levels. We also recommend that systematists should continue to revisit Macrobdella records in natural history collections, which may turn up new evidence of its range, habitat preference, and possible persistence. We conclude by discussing implications of this work for the broader picture of leech conservation in Europe and North America.

Statistical estimates of hominin origination and extinction dates: A case study examining the Australopithecus anamensis–afarensis lineage

Reliable estimates of when hominin taxa originated and went extinct are central to addressing many paleoanthropological questions, including those relating to macroevolutionary patterns. The timing of hominin temporal ranges can be used to test chronological predictions generated from phylogenetic hypotheses. For example, hypotheses of phyletic ancestor–descendant relationships, based on morphological data, predict no temporal range overlap between the two taxa. However, a fossil taxon's observed temporal range is almost certainly underestimated due to the incompleteness of both the fossil record itself and its sampling, and this decreases the likelihood of observing temporal overlap. Here, we focus on a well-known and widely accepted early hominin lineage, Australopithecus anamensis–afarensis, and place 95% confidence intervals (CIs) on its origination and extinction dates. We do so to assess whether its temporal range is consistent with it being a phyletic descendant of Ardipithecus ramidus and/or a direct ancestor to the earliest claimed representative of Homo (i.e., Ledi-Geraru). We find that the last appearance of Ar. ramidus falls within the origination CI of Au. anamensis–afarensis, whereas the claimed first appearance of Homo postdates the extinction CI. These results are consistent with Homo evolving from Au. anamensis–afarensis, but temporal overlap between Ar. ramidus and Au. anamensis–afarensis cannot be rejected at this time. Though additional samples are needed, future research should extend our initial analyses to incorporate the uncertainties surrounding the range endpoints of Ar. ramidus and earliest Homo. Overall, our findings demonstrate the need for quantifying the uncertainty surrounding the appearances and disappearances of hominin taxa in order to better understand the timing of evolutionary events in our clade's history.

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

Abstract Some extinctions have obvious drivers (e.g. over‐harvesting), while others can be less obvious and arise from multiple interacting factors. The extinction of the New Zealand grayling (Prototroctes oxyrhynchus) has been blamed on over‐fishing and predation by introduced trout, but these explanations fail to account for the species disappearance from isolated, uninvaded rivers. We investigated if source–sink dynamics, facilitated by P. oxyrhynchus's amphidromous dispersal habit, could account for the species’ rapid extinction. We created a database of P. oxyrhynchus sightings by surveying newspapers dating back to 1839, along with a review of traditional scientific literature. We used this database to update P. oxyrhynchus's known distribution map and inform sighting models to predict P. oxyrhynchus's extinction date. Finally, we implemented a meta‐population model to explore how source–sink dynamics could interact with off‐take (over‐fishing or predation) to drive extinction. Prototroctes oxyrhynchus was found across New Zealand, except the north of the North Island. Based on sightings methods, the earliest predicted extinction date was 1924, although the species may have persisted until 1972, later than previous estimates have suggested. In the absence of source–sink dynamics, relatively high levels of off‐take were sustainable (up to 30% per generation). When the species was modelled as a panmictic meta‐population including 5% sink habitats, the sustainable off‐take rate was reduced to as low as 5% per generation. Prototroctes oxyrhynchus was a widespread, abundant species that underwent rapid declines and ultimately went extinct. Previous attempts to explain this extinction have failed to account for the species extinction from isolated, pristine rivers. Our modelling shows that treating the species as a panmictic metapopulation and including source–sink dynamics rapidly increases the probability of extinction. We suggest that source–sink dynamics may be an important aspect of the population dynamics of amphidromous species and should be considered when managing taxa with similar dispersal habits.

A fast re-sampling method for using reliability ratings of sightings with extinction-date estimators.

The pattern of sightings of a species that is rare, and then no longer observed, can be used to estimate its extinction date. However, other than physical captures or specimens, the veracity of any sighting is ambiguous, and should be treated probabilistically when used to infer extinction dates. We present a simple yet powerful computational approach for incorporating observational reliability into extinction date estimators (EDE). Our method (1) combines repeated within-year sightings probabilistically, (2) samples observations using reliability as an inclusion probability, (3) infers a probability distribution and summary statistics of extinction dates with any EDE, and (4) computes the frequency distribution of the extinction date. We applied this method to eight exemplar sighting records covering a range of lengths, sighting rates and uncertainties, using a variety of statistical EDEs, and compared these results with a threshold approach for selecting sightings. We also demonstrated a robust coverage of "true" extinction dates based on selected real-world examples of rediscovered species and confirmed extinctions, and simulated sighting records. Our approach represents a powerful generalization of past work because it is not predicated on any specific method for inferring extinction dates, and yet is simple to implement (with R script provided).