Dark extinction: the problem of unknown historical extinctions

The extinction of species before they are discovered and named (dark extinction, DE) is widely inferred as a significant part of species loss in the ‘pre-taxonomic’ period (approx. 1500–1800 CE) and, to some extent, in the ‘taxonomic period’ (approx. 1800–present) as well. The discovery of oceanic islands and other pristine habitats by European navigators and the consequent introduction of destructive mammals, such as rats and goats, started a process of anthropogenic extinction. Much ecosystem change happened before systematic scientific recording, so has led to DE. Statistical methods are available to robustly estimate DE in the ‘taxonomic period’. For the ‘pre-taxonomic period’, simple extrapolation can be used. The application of these techniques to world birds, for example, suggests that approximately 56 DEs occurred in the ‘taxonomic period’ (1800–present) and approximately 180 in the ‘pre-taxonomic period’ (1500–1800). Targeting collection activities in extinction hotspots, to make sure organisms are represented in collections before their extinction, is one way of reducing the number of extinct species without a physical record (providing that collection efforts do not themselves contribute to species extinction).     

Quantifying the extinction vortex

We developed a database of 10 wild vertebrate populations whose declines to extinction were monitored over at least 12 years. We quantitatively characterized the final declines of these well-monitored populations and tested key theoretical predictions about the process of extinction, obtaining two primary results. First, we found evidence of logarithmic scaling of time-to-extinction as a function of population size for each of the 10 populations. Second, two lines of evidence suggested that these extinction-bound populations collectively exhibited dynamics akin to those theoretically proposed to occur in extinction vortices. Specifically, retrospective analyses suggested that a population size of n individuals within a decade of extinction was somehow less valuable to persistence than the same population size was earlier. Likewise, both year-to-year rates of decline and year-to-year variability increased as the time-to-extinction decreased. Together, these results provide key empirical insights into extinction dynamics, an important topic that has received extensive theoretical attention.     

Trophic network models explain instability of Early Triassic terrestrial communities

Studies of the end-Permian mass extinction have emphasized potential abiotic causes and their direct biotic effects. Less attention has been devoted to secondary extinctions resulting from ecological crises and the effect of community structure on such extinctions. Here we use a trophic network model that combines topological and dynamic approaches to simulate disruptions of primary productivity in palaeocommunities. We apply the model to Permian and Triassic communities of the Karoo Basin, South Africa, and show that while Permian communities bear no evidence of being especially susceptible to extinction, Early Triassic communities appear to have been inherently less stable. Much of the instability results from the faster post-extinction diversification of amphibian guilds relative to amniotes. The resulting communities differed fundamentally in structure from their Permian predecessors. Additionally, our results imply that changing community structures over time may explain long-term trends like declining rates of Phanerozoic background extinction.     

Back from the dead II: Thyreophora cynophila (Panzer, 1798) (Diptera: Piophilidae) resurfaces in France after a 183-year-long absence

Summary

Last seen in France in 1836 by Robineau-Desvoidy, the orange-headed necrophagous fly Thyreophora cynophila (Panzer, 1798) has long been considered as extinct. However, it was rediscovered in 2010 in Spain. We report its first sighting in France after a 183-year-long absence. In February 2019, four specimens were collected in southern France (Saint-Paul-de-Jarrat, Ariège), in the Pyrenees.     

On the interpretation and application of mean times to extinction

As a metric of population viability, conservation biologists routinely predict the mean time to extinction (MTE). Interpretation of MTE depends on the underlying distribution of times to extinction (DTE). Despite claims to the contrary, all information regarding extinction risk can be obtained from this single statistic, the MTE, provided the DTE is exponential. We discuss the proper interpretation of MTE and illustrate how to calculate any population viability statistic when only the MTE is known and the DTE is assumed to be exponential. We also discuss the restrictive assumptions underlying the exponential DTE and the conditions under which alternative models for the DTE are preferable to the conventional (exponential) model. Despite superficial similarities between the exponential and alternative DTEs, several key differences can lead to substantially different interpretations of the MTE.     

Light penetrance in lake kinneret

The characteristics of light penetrance in Lake Kinneret, Israel, were observed over the years 1970 to 1973. Light measurements were made concurrently with those of algal speciation and biomass, chlorophyll concentrations and primary production. Vertical extinction coefficients of green light (filter VG9), the most penetrating spectral component, ranged from 0.15 (August 1970) to 0.93 In units m^–1 (April 1970), reflecting the large differences between algal standing crops in non-bloom and bloom seasons. During the dinoflagellate bloom (Peridinium cinctum fa westii) from February through June, the increment of extinction coefficient per unit increase of chlorophyll concentration was 0.006 ln units mg^–1 m². The uneven vertical distribution of algae at this period caused irregularities in the depth curves of light penetrance. At other times, when the phytoplankton cells were more homogeneously dispersed with depth, regular light penetrance curves were observed; however, as previously noted (Rodhe, 1972), attenuation of algal photosynthetic activity often appeared to be regulated by the blue spectral component (filter BG 12). Ratios of absorbed to scattered light in the upper water column ranged from 85:15 to 75:25.     

Clock neurons gate memory extinction in Drosophila

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Correlates of rediscovery and the detectability of extinction in mammals

Extinction is difficult to detect, even in well-known taxa such as mammals. Species with long gaps in their sighting records, which might be considered possibly extinct, are often rediscovered. We used data on rediscovery rates of missing mammals to test whether extinction from different causes is equally detectable and to find which traits affect the probability of rediscovery. We find that species affected by habitat loss were much more likely to be misclassified as extinct or to remain missing than those affected by introduced predators and diseases, or overkill, unless they had very restricted distributions. We conclude that extinctions owing to habitat loss are most difficult to detect; hence, impacts of habitat loss on extinction have probably been overestimated, especially relative to introduced species. It is most likely that the highest rates of rediscovery will come from searching for species that have gone missing during the 20th century and have relatively large ranges threatened by habitat loss, rather than from additional effort focused on charismatic missing species.     

Marine extinction risk shaped by trait–environment interactions over 500 million years

Perhaps the most pressing issue in predicting biotic responses to present and future global change is understanding how environmental factors shape the relationship between ecological traits and extinction risk. The fossil record provides millions of years of insight into how extinction selectivity (i.e., differential extinction risk) is shaped by interactions between ecological traits and environmental conditions. Numerous paleontological studies have examined trait‐based extinction selectivity; however, the extent to which these patterns are shaped by environmental conditions is poorly understood due to a lack of quantitative synthesis across studies. We conducted a meta‐analysis of published studies on fossil marine bivalves and gastropods that span 458 million years to uncover how global environmental and geochemical changes covary with trait‐based extinction selectivity. We focused on geographic range size and life habit (i.e., infaunal vs. epifaunal), two of the most important and commonly examined predictors of extinction selectivity. We used geochemical proxies related to global climate, as well as indicators of ocean acidification, to infer average global environmental conditions. Life‐habit selectivity is weakly dependent on environmental conditions, with infaunal species relatively buffered from extinction during warmer climate states. In contrast, the odds of taxa with broad geographic ranges surviving an extinction (>2500 km for genera, >500 km for species) are on average three times greater than narrow‐ranging taxa (estimate of odds ratio: 2.8, 95% confidence interval = 2.3–3.5), regardless of the prevailing global environmental conditions. The environmental independence of geographic range size extinction selectivity emphasizes the critical role of geographic range size in setting conservation priorities.     

Reduction in animal abundance and oxygen availability during and after the end-Triassic mass extinction

The end-Triassic biodiversity crisis was one of the most severe mass extinctions in the history of animal life. However, the extent to which the loss of taxonomic diversity was coupled with a reduction in organismal abundance remains to be quantified. Further, the temporal relationship between organismal abundance and local marine redox conditions is lacking in carbonate sections. To address these questions, we measured skeletal grain abundance in shallow-marine limestones by point counting 293 thin sections from four stratigraphic sections across the Triassic/Jurassic boundary in the Lombardy Basin and Apennine Platform of western Tethys. Skeletal abundance decreased abruptly across the Triassic/Jurassic boundary in all stratigraphic sections. The abundance of skeletal organisms remained low throughout the lower-middle Hettangian strata and began to rebound during the late Hettangian and early Sinemurian. A two-way ANOVA indicates that sample age (p < .01, η² = 0.30) explains more of the variation in skeletal abundance than the depositional environment or paleobathymetry (p < .01, η² = 0.15). Measured I/Ca ratios, a proxy for local shallow-marine redox conditions, show this same pattern with the lowest I/Ca ratios occurring in the early Hettangian. The close correspondence between oceanic water column oxygen levels and skeletal abundance indicates a connection between redox conditions and benthic organismal abundance across the Triassic/Jurassic boundary. These findings indicate that the end-Triassic mass extinction reduced not only the biodiversity but also the carrying capacity for skeletal organisms in early Hettangian ecosystems, adding to evidence that mass extinction of species generally leads to mass rarity among survivors.     

Proceedings of the SMBE Tri-National Young Investigators' Workshop 2005. What is the role of genome duplication in the evolution of complexity and diversity?

Gene and genome duplications provide a source of genetic material for mutation, drift, and selection to act upon, making new evolutionary opportunities possible. As a result, many have argued that genome duplication is a dominant factor in the evolution of complexity and diversity. However, a clear correlation between a genome duplication event and increased complexity and diversity is not apparent, and there are inconsistencies in the patterns of diversity invoked to support this claim. Interestingly, several estimates of genome duplication events in vertebrates are preceded by multiple extinct lineages, resulting in preduplication gaps in extant taxa. Here we argue that gen(om)e duplication could contribute to reduced risk of extinction via functional redundancy, mutational robustness, increased rates of evolution, and adaptation. The timeline for these processes to unfold would not predict immediate increases in species diversity after the duplication event. Rather, reduced probabilities of extinction would predict a latent period between a genome duplication and its effect on species diversity or complexity. In this paper, we will develop the idea that genome duplication could contribute to species diversity through reduced probability of extinction.     

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.     

Visual learning behaviour in Drosophila melanogaster wildtype AS

Visual learning in Drosophila populations is characterized by a fast rate of acquisition, and conditioning indices near 0.3 are obtained. Heterogeneity of the populations with respect to this behaviour is small. Reversed conditioning is possible. Prolonged extinction procedures fail to reduce the conditioning index to zero. Memory lasts for a minimum of 14 hours.     

ApoE isoform‐dependent deficits in extinction of contextual fear conditioning

The three major human apoE isoforms (apoE2, apoE3 and apoE4) are encoded by distinct alleles (?2, ?3 and ?4). Compared with ?3, ?4 is associated with increased risk to develop Alzheimer's disease (AD), cognitive impairments in Parkinson's disease (PD), and other conditions. In contrast, a recent study indicated an increased susceptibility to the recurring and re‐experiencing symptom cluster of Post‐Traumatic Stress Disorder (PTSD), as well as related memory impairments, in patients carrying at least one ?2 allele. Contextual fear conditioning and extinction are used in human and animal models to study this symptom cluster. In this study, acquisition (day 1, training), consolidation (day 2, first day of re‐exposure) and extinction (days 2–5) of conditioned contextual fear in human apoE2, apoE3 and apoE4 targeted replacement and C57BL/6J wild‐type (WT) mice was investigated. Male and female apoE2 showed acquisition and retrieval of conditioned fear, but failed to exhibit extinction. In contrast, WT, apoE3 and apoE4 mice showed extinction. While apoE2 mice exhibited lower freezing in response to the context on day 2 than apoE3 and apoE4 mice, this cannot explain their extinction deficit as WT mice exhibited similar freezing levels as apoE2 mice on day 2 but still exhibited extinction. Elevating freezing through extended training preserved extinction in controls, but failed to ameliorate extinction deficits in apoE2 animals. These data along with clinical data showing an association of apoE2 with susceptibility to specific symptom clusters in PTSD supports an important role for apoE isoform in the extinction of conditioned fear.     

Distinguishing Extinction and Natural Selection in the Anthropocene: Preventing the Panda Paradox through Practical Education Measures

In the midst of only the 6th mass extinction in the Earth's history, we must rethink how we teach evolution to prevent natural selection from being incorrectly used as a biological justification for inaction in the face of today's human-caused mass extinction crisis. Pundits, policy makers, and the general public regularly identify the extinction of endangered species as natural selection at work, rather than attributing modern-day extinction to the sudden catastrophic bad luck of human caused environmental change, a phenomenon distinct from natural selection. In this natural selection framing, the inability of species to survive in human altered environments is the normal progression of “survival of the fittest” and conservation measures designed to protect species is human interference with natural selection. Paradoxically, this erroneous framing of extinction as the normal course of natural selection ignores humanity's exceptional role in causing today's mass extinction crisis. Our examination of this issue in U.S. college students indicates that it arises from misunderstanding the role of extinction in the history of life, leading us to recommend a greater teaching emphasis on the distinction between extinction and natural selection, and on past mass extinction events. Also see the video abstract here https://youtu.be/29VRyirMdiw     

Frustration Behaviors in Domestic Dogs

During extinction a previously learned behavior stops being reinforced. In addition to the decrease in the rate of the instrumental response, it produces an aversive emotional state known as frustration. This state can be assimilated with the fear reactions that occur after aversive stimuli are introduced at both the physiological and behavioral levels. This study evaluated frustration reactions of domestic dogs (Canis familiaris) during a communicative situation involving interactions with a human. The task included the reinforcement and extinction of the gaze response toward the experimenter's face when the dogs tried to obtain inaccessible food. The dog's frustration reactions during extinction involved an increase in withdrawal and side orientation to the location of the human as well as lying down, ambulation, sniffing, and vocalizations compared with the last acquisition trial. These results are especially relevant for domestic dog training situations in which the extinction technique is commonly used to discourage undesirable behaviors.