Estimating How Many Undescribed Species Have Gone Extinct

Biodiversity indices often combine data from different species when used in monitoring programs. Heuristic properties can suggest preferred indices, but we lack objective ways to discriminate between indices with similar heuristics. Biodiversity indices can be evaluated by determining how well they reflect management objectives that a monitoring program aims to support. For example, the Convention on Biological Diversity requires reporting about extinction rates, so simple indices that reflect extinction risk would be valuable. We developed 3 biodiversity indices that are based on simple models of population viability that relate extinction risk to abundance. We based the first index on the geometric mean abundance of species and the second on a more general power mean. In a third index, we integrated the geometric mean abundance and trend. These indices require the same data as previous indices, but they also relate directly to extinction risk. Field data for butterflies and woodland plants and experimental studies of protozoan communities show that the indices correlate with local extinction rates. Applying the index based on the geometric mean to global data on changes in avian abundance suggested that the average extinction probability of birds has increased approximately 1% from 1970 to 2009.Conectando Índices para el Monitoreo de la Biodiversidad con la Teoría de Riesgo de ExtinciónResumenLos índices de biodiversidad combinan frecuentemente los datos de diferentes especies cuando se usan en los programas de monitoreo. Las propiedades heurísticas pueden sugerir índices preferidos, pero carecemos de medios objetivos para discriminar a los índices con propiedades heurísticas similares. Los índices de biodiversidad pueden evaluarse al determinar qué tan bien reflejan los objetivos de manejo que un programa de monitoreo busca apoyar. Por ejemplo, la Convención sobre la Diversidad Biológica requiere reportar las tasas de extinción, así que los índices que reflejan el riesgo de extinción serían valiosos. Desarrollamos 3 índices de biodiversidad que se basan en modelos sencillos de viabilidad de población y que relacionan el riesgo de extinción con la abundancia. Basamos el primer índice en la media geométrica de la abundancia de especies, y el segundo en una media de poder más general. En el tercer índice integramos la media geométrica y la tendencia. Estos índices requieren los mismos datos que índices previos, pero también se relacionan directamente con el riesgo de extinción. La información de campo sobre mariposas y plantas de bosque, y los estudios experimentales de comunidades protozoarias, muestran que los índices se correlacionan con las tasas locales de extinción. Al aplicar el índice basado en la media geométrica sobre los datos globales de los cambios en la abundancia de aves, sugirió que la probabilidad de extinción promedio de aves ha incrementado aproximadamente 1% desde 1970 hasta 2009.Palabras ClaveÍndice de biodiversidad, media geométrica, medida de la biodiversidad, riesgo de extinción

A first analysis of the stability of trophic structure following tropical forest fragmentation was performed in an experimentally fragmented tropical forest landscape in Central Amazonia. A taxonomically and trophically diverse assemblage of 993 species of beetles was sampled from 920 m 2 of leaf litter at 46 sites varying in distance from forest edge and fragment area. Beetle density increased significantly towards the forest edge and showed non-linear changes with fragment area, due to the influx of numerous disturbed-area species into 10 ha and 1 ha fragments. There was a marked change in species composition with both decreasing distance from forest edge and decreasing fragment area, but surprisingly this change in composition was not accompanied by a change in species richness. Rarefied species richness did not vary significantly across any of the sites, indicating that local extinctions of deep forest species were balanced by equivalent colonization rates of disturbed-area species. The change in species composition with fragmentation was non-random across trophic groups. Proportions of predator species and xylophage species changed significantly with distance from forest edge, but no area-dependent changes in proportions of species in trophic groups were observed. Trophic structure was also analysed with respect to proportions of abundance in six trophic groups. Proportions of abundance of all trophic groups except xylomycetophages changed markedly with respect to both distance from forest edge and fragment area. Local extinction probabilities calculated for individual beetle species supported theoretical predictions of the differential susceptibility of higher trophic levels to extinction, and of changes in trophic structure following forest fragmentation. To reduce random effects due to sampling error, only abundant species ( n ≥ 46) were analysed for extinction probabilities, as defined by absence from samples. Of these common species, 27% had significantly higher probabilities of local extinction following fragmentation. The majority of these species were predators; 42% of all abundant predator species were significantly more likely to be absent from samples in forest fragments than in undisturbed forest. These figures are regarded as minimum estimates for the entire beetle assemblage because rarer species will inevitably have higher extinction probabilities. Absolute loss of biodiversity will affect ecosystem process rates, but the differential loss of species from trophic groups will have an even greater destabilizing effect on food web structure and ecosystem function.

ABSTRACTAim To examine temporal variation in nestedness and whether nestedness patterns predict colonization, extinction and turnover across islands and species.Location Dahlak Archipelago, Red Sea.Method The distributions of land birds on 17 islands were recorded in two periods 30 years apart. Species and islands were reordered in the Nestedness Temperature Calculator, software for assessing degrees of nestedness in communities. The occupancy probability of each cell, i.e. species–island combinations, was calculated in the nested matrix and an extinction curve (boundary line) was specified. We tested whether historical and current nested ranks of species and islands were correlated, whether there was a relationship between occupancy probability (based on the historical data) and number of extinctions or colonizations (regression analyses) and whether the boundary line could predict extinctions and colonizations (chi‐square analyses).Results Historical and current nested ranks of islands and species were correlated but changes in occupancy patterns were common, particularly among bird species with intermediate incidence. Extinction and turnover of species were higher for small than large islands, and colonization was negatively related to isolation. As expected, colonizations were more frequent above than below the boundary line. Probability of extinction was highest at intermediate occupancy probability, giving a quadratic relationship between extinction and occupancy probability. Species turnover was related to the historical nested ranks of islands. Colonization was related negatively while extinction and occupancy turnover were related quadratically to historical nested ranks of species.Main conclusions Some patterns of the temporal dynamics agreed with expectations from nested patterns. However, the accuracy of the predictions may be confounded by regional dynamics and distributions of idiosyncratic, resource‐limited species. It is therefore necessary to combine nestedness analysis with adequate knowledge of the causal factors and ecology of targeted species to gain insight into the temporal dynamics of assemblages and for nestedness analyses to be helpful in conservation planning.

Soil macrofaunal biodiversity in Amazonian pastures: Matching sampling with patterns

Metapopulation ecology is a field that is richer in theory than in empirical results. Many existing empirical studies use an incidence function approach based on spatial patterns and key assumptions about extinction and colonization rates. Here we recast these assumptions as hypotheses to be tested using 18 years of historic detection survey data combined with four years of data from a new monitoring program for the Lower Keys marsh rabbit. We developed a new model to estimate probabilities of local extinction and colonization in the presence of nondetection, while accounting for estimated occupancy levels of neighboring patches. We used model selection to identify important drivers of population turnover and estimate the effective neighborhood size for this system. Several key relationships related to patch size and isolation that are often assumed in metapopulation models were supported: patch size was negatively related to the probability of extinction and positively related to colonization, and estimated occupancy of neighboring patches was positively related to colonization and negatively related to extinction probabilities. This latter relationship suggested the existence of rescue effects. In our study system, we inferred that coastal patches experienced higher probabilities of extinction and colonization than interior patches. Interior patches exhibited higher occupancy probabilities and may serve as refugia, permitting colonization of coastal patches following disturbances such as hurricanes and storm surges. Our modeling approach should be useful for incorporating neighbor occupancy into future metapopulation analyses and in dealing with other historic occupancy surveys that may not include the recommended levels of sampling replication.

Mangrove species are uniquely adapted to tropical and subtropical coasts, and although relatively low in number of species, mangrove forests provide at least US $1.6 billion each year in ecosystem services and support coastal livelihoods worldwide. Globally, mangrove areas are declining rapidly as they are cleared for coastal development and aquaculture and logged for timber and fuel production. Little is known about the effects of mangrove area loss on individual mangrove species and local or regional populations. To address this gap, species-specific information on global distribution, population status, life history traits, and major threats were compiled for each of the 70 known species of mangroves. Each species' probability of extinction was assessed under the Categories and Criteria of the IUCN Red List of Threatened Species. Eleven of the 70 mangrove species (16%) are at elevated threat of extinction. Particular areas of geographical concern include the Atlantic and Pacific coasts of Central America, where as many as 40% of mangroves species present are threatened with extinction. Across the globe, mangrove species found primarily in the high intertidal and upstream estuarine zones, which often have specific freshwater requirements and patchy distributions, are the most threatened because they are often the first cleared for development of aquaculture and agriculture. The loss of mangrove species will have devastating economic and environmental consequences for coastal communities, especially in those areas with low mangrove diversity and high mangrove area or species loss. Several species at high risk of extinction may disappear well before the next decade if existing protective measures are not enforced.

Human induced global change has greatly altered the structure and composition of food webs through the invasion of non‐native species and the extinction of native species. Much attention has been paid to the effects of species deletions on food web structure and stability. However, recent empirical evidence suggests that for most taxa local species richness has increased as successful invasions outpace extinctions at this scale. This pattern suggests that food webs, which represent feeding interactions at the local scale, may be increasing in species richness. Knowledge of how food web structure relates to invasive species establishment and the effect of successful invaders on subsequent food web structure remains an unknown but potentially important aspect of global change. Here we explore the effect of food web topology on invasion success in model food webs to develop hypotheses about how the distribution of biodiversity across trophic levels affects the success of invasion at each trophic level. Our results suggest a connectance (C) based framework for predicting invasion success in food webs due to the way that C constrains the number of species at each trophic level and thus the number of potential predators and prey for an invader at a given trophic level. We use the relationship between C and the proportion of species at each trophic level in 14 well studied food webs to make the following predictions; 1) the success of basal invaders will increase as C increases due to the decrease in herbivores in high C webs, 2) herbivore invasion success will decrease as C increases due to the decrease in the proportion of basal species and increase in intermediate species and omnivores in high C webs. 3) Top predator invasion success will increase as C increases due to the increase in intermediate prey species. However, it is not clear how the relative influence of trophic structure compares to empirically known predictors of invasion success such as invader traits, propagule pressure, and resource availability.

There are too many kinds of organisms to be able to study and manage each, yet the loss of a single species can sometimes unravel an ecosystem. Such `fusewire species'– critical in the same sense that an electrical fuse can cut out a whole circuit – would be a rewarding focus for research and management effort. However, this approach can only be effective if these `fusewires' represent but a small proportion of the number of species in the system.AimTo demonstrate methods for measuring what proportion of the species in a system are critical to ecosystem function.MethodsThe prevalence of fusewire species was measured in manipulative experiments on an aquatic microcosm.ResultsNo single genus deletion caused changes in key characteristics of the system.Main conclusionsComparison of these results with other published studies shows that the proportion of critical fusewire species varies amongst different ecosystems. The oxidation pond microcosms were shown to contain no single species indispensable to system function. They appear to be ill‐suited to a management strategy which focuses on priority eukaryote species. However, a single study provides no evidence that this result is general or even typical of other kinds of ecosystems; it is presented here as an empirical model. Other methods of investigation are available; they are less experimentally rigorous but more practical. These could provide important guidance in planning an approach to management in a particular ecosystem.

In den Tropen bedingen anthropogene Veränderungen natürlicher Habitate gegenwärtig einen nie da gewesenen Verlust der Biodiversität. Agrarforsten tropischer Landschaften, mit traditionellem Schattenbaumbestand, repräsentieren in immer größerem Maße die einzigen Habitate mit einem ausreichenden Baumbestand und unterstützen somit hohe Biodiversitätsraten. Umfassend werden in den Tropen Agrarforsten mit heterogenem Schattenbaumbestand in homogene, unbeschattete Systeme umgewandelt. Diese großräumigen Vereinheitlichungen der Lebensräume im Dienste steigernder Produktivität, bedrohen jedoch sowohl Biodiversität, als auch wichtige ökologische Prozesse, die ihrerseits Bestäubung der Nutzpflanzen, Schädlingsbefall und Nachhaltigkeit der Landnutzung beeinflussen.In unserer Studie untersuchten wir den Umfang, in welchem durch Kakao dominierte Agrarforsten zur Erhaltung der Diversität von Insekten beitragen können. Zur Einzuschätzung der direkten und indirekten Faktoren, welche die Käfer- und Ameisendiversität beeinflussen, dienten uns Agrarforsten mit unterschiedlicher Zusammensetzungen des Schattenbaumbestandes. Gleichzeitig beobachteten wir die Wechselbeziehungen von Kakao-Schädlingen und Kakao-Bestäubern in Bezug zu den unterschiedlich bewirtschafteten Agroforsten.

Testing hypotheses of differential mammalian extinctions subsequent to the Great American biotic interchange

According to when they attained high diversity, major taxa of marine animals have been clustered into three groups, the Cambrian, Paleozoic, and Modern Faunas. Because the Cambrian Fauna was a relatively minor component of the total fauna after mid-Ordovician time, the Phanerozoic history of marine animal diversity is largely a matter of the fates of the Paleozoic and Modern Faunas. The fact that most late Cenozoic genera belong to taxa that have been radiating for tens of millions of years indicates that the post-Paleozoic increase in diversity indicated by fossil data is real, rather than an artifact of improvement of the fossil record toward the present.Assuming that ecological crowding produced the so-called Paleozoic plateau for family diversity, various workers have used the logistic equation of ecology to model marine animal diversification as damped exponential increase. Several lines of evidence indicate that this procedure is inappropriate. A plot of the diversity of marine animal genera through time provides better resolution than the plot for families and has a more jagged appearance. Generic diversity generally increased rapidly during the Paleozoic, except when set back by pulses of mass extinction. In fact, an analysis of the history of the Paleozoic Fauna during the Paleozoic Era reveals no general correlation between rate of increase for this fauna and total marine animal diversity. Furthermore, realistically scaled logistic simulations do not mimic the empirical pattern. In addition, it is difficult to imagine how some fixed limit for diversity could have persisted throughout the Paleozoic Era, when the ecological structure of the marine ecosystem was constantly changing. More fundamentally, the basic idea that competition can set a limit for marine animal diversity is incompatible with basic tenets of marine ecology: predation, disturbance, and vagaries of recruitment determine local population sizes for most marine species. Sparseness of predators probably played a larger role than weak competition in elevating rates of diversification during the initial (Ordovician) radiation of marine animals and during recoveries from mass extinctions. A plot of diversification against total diversity for these intervals yields a band of points above the one representing background intervals, and yet this band also displays no significant trend (if the two earliest intervals of the initial Ordovician are excluded as times of exceptional evolutionary innovation). Thus, a distinctive structure characterized the marine ecosystem during intervals of evolutionary radiation—one in which rates of diversification were exceptionally high and yet increases in diversity did not depress rates of diversification.Particular marine taxa exhibit background rates of origination and extinction that rank similarly when compared with those of other taxa. Rates are correlated in this way because certain heritable traits influence probability of speciation and probability of extinction in similar ways. Background rates of origination and extinction were depressed during the late Paleozoic ice age for all major marine invertebrate taxa, but remained correlated. Also, taxa with relatively high background rates of extinction experienced exceptionally heavy losses during biotic crises because background rates of extinction were intensified in a multiplicative manner; decimation of a large group of taxa of this kind in the two Permian mass extinctions established their collective identity as the Paleozoic Fauna.Characteristic rates of origination and extinction for major taxa persisted from Paleozoic into post-Paleozoic time. Because of the causal linkage between rates of origination and extinction, pulses of extinction tended to drag down overall rates of origination as well as overall rates of extinction by preferentially eliminating higher taxa having relatively high background rates of extinction. This extinction/origination ratchet depressed turnover rates for the residual Paleozoic Fauna during the Mesozoic Era. A decline of this fauna's extinction rate to approximately that of the Modern Fauna accounts for the nearly equal fractional losses experienced by the two faunas in the terminal Cretaceous mass extinction.Viewed arithmetically, the fossil record indicates slow diversification for the Modern Fauna during Paleozoic time, followed by much more rapid expansion during Mesozoic and Cenozoic time. When viewed more appropriately as depicting geometric—or exponential—increase, however, the empirical pattern exhibits no fundamental secular change: the background rate of increase for the Modern Fauna—the fauna that dominated post-Paleozoic marine diversity—simply persisted, reflecting the intrinsic origination and extinction rates of constituent taxa. Persistence of this overall background rate supports other evidence that the empirical record of diversification for marine animal life since Paleozoic time represents actual exponential increase. This enduring rate makes it unnecessary to invoke environmental change to explain the post-Paleozoic increase of marine diversity.Because of the resilience of intrinsic rates, an empirically based simulation that entails intervals of exponential increase for the Paleozoic and Modern Faunas, punctuated by mass extinctions, yields a pattern that is remarkably similar to the empirical pattern. It follows that marine animal genera and species will continue to diversify exponentially long into the future, barring disruption of the marine ecosystem by human-induced or natural environmental changes.

We present an individual‐based model of the Norwegian wolf Canis lupus population, which is used to evaluate the effectiveness of current and potential management policies in fulfilling the Norwegian Government's stated aim of maintaining three breeding packs within a designated wolf zone. The model estimates the ‘functional extinction rate’ of the population, defined as the proportion of years in which breeding wolf packs are absent. Under the current conditions according to estimates from Scandinavia, with observed values of natural survival rates (0.903) and unauthorised mortality (0.203) and allowing for immigration from Sweden, the model predicts that the probability of functional extinction is as low as 0.07. This output variable is highly sensitive to the demographic parameters, and if alternative estimates of natural survival rates (0.73 for cubs and 0.83 for adults) reported for wolves elsewhere and higher rates of unauthorised mortality (0.4) are utilised, the functional extinction rate is 0.67 ± 0.15, and the population is dependent on maintenance by immigration from Sweden. The main determinants of the functional extinction rate are the unauthorised mortality rate and the immigration rate from Sweden. The Scandinavian population as a whole shows a rapid non‐linear increase in probability of extinction at unauthorised mortality rates >0.10. Varying levels of the current management interventions (increasing the size of the wolf zone and target number of packs) are ineffective; only when the unauthorised mortality rate falls below 0.30 is a self‐sustaining population in Norway able to establish. An adaptive harvest policy with culls targeted only at dispersing animals, or taking place only when the population exceeds a threshold level, could be sustainable if the unauthorised mortality rate is reduced. The fact that the Norwegian Government has been explicit about its management strategy and objectives has allowed us to test the ability of this strategy to meet the objectives, and we have shown that it is dependant upon maintaining the current circumstances alongside a high adult survival rate to be able to do so. Given the potentially critical role of the Swedish population in sustaining Norway's wolves, there is a strong case for joint management of the Scandinavian population. These insights are likely to be relevant for the management of other species living across geopolitical boundaries.

Summary The effect that the surrounding landscape matrix has on the loss of species from fragmented patches remains largely unknown. To determine whether there were differences in the persistence of plants inhabiting remnant patches in contrasting landscape types we examined the local extinction of grassland plants along an urban–rural gradient in western Victoria, Australia. Thirty small grassland remnants that had been comprehensively surveyed between 1979 and 1990 were intensively re‐surveyed. A total of 289 (26%) of the 1104 plant populations present in the 1980s were not relocated and were presumed to be locally extinct. The proportion of populations lost differed along the gradient, with higher local extinction rates at patches in urban (37%) and peri‐urban landscapes (27%) than those in the rural landscape (20%). We calculated the probability of local extinction of species in urban, peri‐urban and rural landscapes using Bayesian logistic regression models. Across all plant functional traits examined, species had a consistently higher probability of local extinction in the urban landscape. Species that were geophytes or hemicryptophytes with a flat rosette and species with seeds dispersed by wind or ants had substantially increased risks of extinction in the urban landscape. Low seed mass, the lack of vegetative reproduction and the presence of a soil‐stored seed bank increased the probability of local extinction in all landscapes. Regionally rare species had a higher probability of local extinction in rural and peri‐urban landscapes but rarity had little influence on extinction risk in urban landscapes. Urbanization has a strong influence on the species composition of urban grasslands and substantially increases the probability of local extinction of plants with particular combinations of functional traits.

We carried out an intensive and systematized sampling of the spider fauna of the tropical mountain cloud forest (TMCF) in El Triunfo Biosphere Reserve, Chiapas, Mexico, in order to analyze their composition, species richness, abundance, and proportion of undescribed species, and to compare these results with those found in other TMCFs. We sampled ten plots in two seasons (dry and rainy) using different sampling techniques on two strata (ground and understory). A total of 7,432 specimens were collected corresponding to 28 families, 78 genera and 111 morphospecies. A high proportion of total species (58.6%) were undescribed species. For 11 species originally described from a single sex, we found the other sex. Five species and one genus were new records for the Mexican spider fauna. Understory stratum had higher numbers of species and individuals than ground stratum, and there was a high species turnover, with only 17% of the total species shared between strata. The spider fauna of El Triunfo shows similarities with other TMCFs (especially that on the same mountain range) concerning the identities of dominant and species-rich families, family and genera composition, the presence and relevance (in abundance or richness) of families that are uncommon in lowland tropical habitats (Linyphiidae and Theridiosomatidae), and in the high proportion of undescribed species. However, there is a high species turnover among sites (only 16% species shared), even at relatively short distances, that seems derived in part from the relative high proportions of endemic species. Our results suggest that high abundance of Theridiosomatidae and Linyphiidae, together with high species richness of this last family, could be used as conservation indicators for the Mexican TMCFs. The high numbers of undescribed species in the analyzed TMCFs, and their relatively high endemicity levels, support that TMCFs could be regarded as hotspots for the order Araneae.

The relationship between food web complexity and stability has been the subject of a long‐standing debate in ecology. Although rapid changes in the food web structure through adaptive foraging behavior can confer stability to complex food webs, as reported by Kondoh (Science 299:1388–1391, ), the exact mechanisms behind this adaptation have not been specified in previous studies; thus, the applicability of such predictions to real ecosystems remains unclear. One mechanism of adaptive foraging is evolutionary change in genetically determined prey use. We constructed individual‐based models of evolution of prey use by predators assuming explicit population genetics processes, and examined how this evolution affects the stability (i.e., the proportion of species that persist) of the food web and whether the complexity of the food web increased the stability of the prey–predator system. The analysis showed that the stability of food webs decreased with increasing complexity regardless of evolution of prey use by predators. The effects of evolution on stability differed depending on the assumptions made regarding genetic control of prey use. The probabilities of species extinctions were associated with the establishment or loss of trophic interactions via evolution of the predator, indicating a clear link between structural changes in the food web and community stability.