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.     

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).     

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.     

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.     

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.     

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.     

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.     

Taxon age,origination, and extinction through geologic time

Changes in the taxon ages of fossil marine families that are alive and those that become extinct in each stage of the Phanerozoic reflect changes in the origination rate, differences in the extinction rate of families with different taxon ages, and mass extinction events. Extinct families are generally much younger than the population from which they were drawn. Periods dominated by higher numbers of younger families are more susceptible to larger size extinctions and greater variation in extinction size. As a result the relative size of extinction peaks must be viewed with regard to the taxon age structure of the population. Mass extinctions cause little change in the taxon age of the fauna. However, adaptive radiations cause a large drop in the average age of the families that are alive at any given time. Families must be treated as dynamic entities in macroevolutionary studies because their probabilities of extinction change over time.     

INFERRING THE RATES OF BRANCHING AND EXTINCTION FROM MOLECULAR PHYLOGENIES

Molecular techniques provide ancestral phylogenies of extant taxa with estimated branching times. Here we studied the pattern of ancestral phylogeny of extant taxa produced by branching (or cladogenesis) and extinction of taxa, assuming branching processes with time-dependent rates. (1) If the branching rate b and extinction rate c are constant, the semilog plot of the number of ancestral lineages over time is not a straight line but is curvilinear, with increasing slope toward the end, implying that ancestral phylogeny shows apparent increase in the branching rate near the present. The estimate of b and c based on nonlinear fitting is examined by computer simulation. The estimate of branching rate can be usable for a large phylogeny if b is greater than c, but the estimate of extinction rate c is unreliable because of large bias and variance. (2) Gradual decrease in the slope of the semilog plot of the number of ancestral lineages over time, as was observed in a phylogeny of bird families based on DNA hybridization data, can be explained equally well by either the decreasing branching rate or the increasing extinction rate. Infinitely many pairs of branching and extinction rates as functions of time can produce the same ancestral phylogeny. (3) An explosive branching event in the past would appear as a quick increase in the number of ancestral lineages. In contrast, mass extinction occurring in a brief period, if not accompanied by an increase in branching rate, does not produce any rapid change in the number of ancestral lineages at the time. (4) The condition in which the number of ancestral lineages of extant species changes in parallel with the actual number of species in the past is derived.     

Clock neurons gate memory extinction in Drosophila

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Chaotic dynamics may determine the effect of inter-patch migration on metapopulation survival

A simple, strategic model of a system of habitat fragments connected by conservation corridors is presented. The intrinsic dynamics of the population on each fragment are stochastic. In addition, at each generation there is a probability of a catastrophic event occurring which affects all the habitat fragments by greatly reducing the size of the population on each. Global extinction is considered to occur when all the populations simultaneously fall below a threshold value. If the intrinsic dynamics on each fragment are simple cycles or a stable equilibrium, then the addition of conservation corridors does not reduce the frequency of global extinction. This is because migration between fragments induces their populations to have values which are similar to each other. However, if the intrinsic population dynamics are chaotic then the probability of global extinction is greatly reduced by the introduction of conservation corridors. Although local extinction is likely, the chaos acts to oppose the synchronising effect of migration. Often a subset of the populations survive a catastrophe and can recolonize the other patches.     

Reconstructing past species assemblages reveals the changing patterns and drivers of extinction through time

Predicting future species extinctions from patterns of past extinctions or current threat status relies on the assumption that the taxonomic and biological selectivity of extinction is consistent through time. If the driving forces of extinction change through time, this assumption may be unrealistic. Testing the consistency of extinction patterns between the past and the present has been difficult, because the phylogenetically explicit methods used to model present-day extinction risk typically cannot be applied to the data from the fossil record. However, the detailed historical and fossil records of the New Zealand avifauna provide a unique opportunity to reconstruct a complete, large faunal assemblage for different periods in the past. Using the first complete phylogeny of all known native New Zealand bird species, both extant and extinct, we show how the taxonomic and phylogenetic selectivity of extinction, and biological correlates of extinction, change from the pre-human period through Polynesian and European occupation, to the present. These changes can be explained both by changes in primary threatening processes, and by the operation of extinction filter effects. The variable patterns of extinction through time may confound attempts to identify risk factors that apply across time periods, and to infer future species declines from past extinction patterns and current threat status.     

Lessons from a kill

During their colonization by Polynesians and later by Europeans, the Hawaiian islands suffered a massive loss of species. All the extinctions are indirectly attributable to human impact. Nonetheless, it has proved extremely difficult to specify which of several possible mechanisms caused each particular extinction. This seems to admit defeat in the battle to understand past extinctions. Such understanding could guide our efforts to protect species that are now threatened with extinction. Will it be easier to understand the causes of future extinctions? Surveys of future extinctions stress habitat destruction as the simple and dominant mechanism. This contrasts to its secondary (and generally confused) role in past extinctions. I argue that this contrast between the complexity of the past and the apparent simplicity of the future arises because extinction mechanisms are inherently synergistic. Once extensive species losses begin, it may be impossible to separate the mechanisms and thus manage an individual species as if its decline had a single cause.     

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.     

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.     

Scaling the extinction vortex: Body size as a predictor of population dynamics close to extinction events

1. Mutual reinforcement between abiotic and biotic factors can drive small populations into a catastrophic downward spiral to extinction—a process known as the “extinction vortex.” However, empirical studies investigating extinction dynamics in relation to species'' traits have been lacking.
2. We assembled a database of 35 vertebrate populations monitored to extirpation over a period of at least ten years, represented by 32 different species, including 25 birds, five mammals, and two reptiles. We supplemented these population time series with species‐specific mean adult body size to investigate whether this key intrinsic trait affects the dynamics of populations declining toward extinction.
3. We performed three analyses to quantify the effects of adult body size on three characteristics of population dynamics: time to extinction, population growth rate, and residual variability in population growth rate.
4. Our results provide support for the existence of extinction vortex dynamics in extirpated populations. We show that populations typically decline nonlinearly to extinction, while both the rate of population decline and variability in population growth rate increase as extinction is approached. Our results also suggest that smaller‐bodied species are particularly prone to the extinction vortex, with larger increases in rates of population decline and population growth rate variability when compared to larger‐bodied species.
5. Our results reaffirm and extend our understanding of extinction dynamics in real‐life extirpated populations. In particular, we suggest that smaller‐bodied species may be at greater risk of rapid collapse to extinction than larger‐bodied species, and thus, management of smaller‐bodied species should focus on maintaining higher population abundances as a priority.

     

Sexual cannibalism and population viability

Some behaviours that typically increase fitness at the individual level may reduce population persistence, particularly in the face of environmental changes. Sexual cannibalism is an extreme mating behaviour which typically involves a male being devoured by the female immediately before, during or after copulation, and is widespread amongst predatory invertebrates. Although the individual‐level effects of sexual cannibalism are reasonably well understood, very little is known about the population‐level effects. We constructed both a mathematical model and an individual‐based model to predict how sexual cannibalism might affect population growth rate and extinction risk. We found that in the absence of any cannibalism‐derived fecundity benefit, sexual cannibalism is always detrimental to population growth rate and leads to a higher population extinction risk. Increasing the fecundity benefits of sexual cannibalism leads to a consistently higher population growth rate and likely a lower extinction risk. However, even if cannibalism‐derived fecundity benefits are large, very high rates of sexual cannibalism (>70%) can still drive the population to negative growth and potential extinction. Pre‐copulatory cannibalism was particularly damaging for population growth rates and was the main predictor of growth declining below the replacement rate. Surprisingly, post‐copulatory cannibalism had a largely positive effect on population growth rate when fecundity benefits were present. This study is the first to formally estimate the population‐level effects of sexual cannibalism. We highlight the detrimental effect sexual cannibalism may have on population viability if (1) cannibalism rates become high, and/or (2) cannibalism‐derived fecundity benefits become low. Decreased food availability could plausibly both increase the frequency of cannibalism, and reduce the fecundity benefit of cannibalism, suggesting that sexual cannibalism may increase the risk of population collapse in the face of environmental change.     

Millennial-scale faunal record reveals differential resilience of European large mammals to human impacts across the Holocene

The use of short-term indicators for understanding patterns and processes of biodiversity loss can mask longer-term faunal responses to human pressures. We use an extensive database of approximately 18 700 mammalian zooarchaeological records for the last 11 700 years across Europe to reconstruct spatio-temporal dynamics of Holocene range change for 15 large-bodied mammal species. European mammals experienced protracted, non-congruent range losses, with significant declines starting in some species approximately 3000 years ago and continuing to the present, and with the timing, duration and magnitude of declines varying individually between species. Some European mammals became globally extinct during the Holocene, whereas others experienced limited or no significant range change. These findings demonstrate the relatively early onset of prehistoric human impacts on postglacial biodiversity, and mirror species-specific patterns of mammalian extinction during the Late Pleistocene. Herbivores experienced significantly greater declines than carnivores, revealing an important historical extinction filter that informs our understanding of relative resilience and vulnerability to human pressures for different taxa. We highlight the importance of large-scale, long-term datasets for understanding complex protracted extinction processes, although the dynamic pattern of progressive faunal depletion of European mammal assemblages across the Holocene challenges easy identification of ‘static’ past baselines to inform current-day environmental management and restoration.