Increased Extinction Rates Research Articles

Impact of Climate Change and Global Warming on Crop Pollinators and their Mitigation Strategies: A Review

Climate change and global warming are of great concern to agriculture worldwide and are among the most debated and discussed issues in today’s civilization. Climate change at the global level is leading to increased habitat loss, geographical shifts and increased extinction rates of biodiversity. The production of some crops like fruits and vegetables is dependent upon pollination by crop pollinators: bee and non-bee pollinators. Animal-based pollination puts up to 30% of global food production and bee-pollinated crops contribute to approximately one-third of the total human dietary supply. Nearly 75 percent of the world’s food plants show increased fruit or seed set with insect visitation. The economic value of these services is estimated to be around 153 billion dollars per annum. If there is an increase in the average global temperature by 1.5-2.5°C, then approximately 20-30 percent of the known species will be threatened which may lead to mass extinction. As a result, there is a serious risk of economic losses as well as challenges to human food security. Only 11 of the 20,000-30,000 species of bee are managed by farmers. Pollination by honeybees and wild bees significantly increased yield quantity and quality averaging up to 62%, while exclusion of pollinators caused an average yield gap of 37% in cotton and 59% in sesame. In India, studies carried out by the International Centre for Integrated Mountain Development revealed that apple productivity has declined as a result of inadequate pollination.

Inferring the evolutionary history of the Sino-Himalayan biodiversity hotspot using a Bayesian birth–death skyline model

The current status of the Sino-Himalayan region as a biodiversity hotspot, particularly for flora, has often been linked to the uplift of the Sino-Tibetan Plateau and Himalayan and Hengduan Mountains. However, the relationship between the topological development of the region and the onset of diversification is yet to be confirmed. Here, we apply Bayesian phylodynamic methods to a large phylogeny of angiosperm species from the Sino-Himalayas to infer changes in their rates of evolution through time. We find strong evidence for high diversification rates in the Paleocene, late Miocene and Pliocene, and for negative diversification rates in the Quaternary driven by an increase in extinction rates. Our analyses suggest that changes in global palaeotemperatures are unlikely to be a driving force for these rate shifts. Instead, the collision of the Indian continent with Eurasia and coeval topographic change in the Sino-Himalayas, the Miocene Grassland Expansion and the impact of Pleistocene glaciations on this altitudinally variable region may have driven these rates. We also demonstrate the strong influence of the choice of change times on the shape of inferred piecewise-constant trajectories in Bayesian phylodynamics, and advocate for the use of prior information when making this decision.

Habitat preference of common minke whale (Balaenoptera acutorostrata) in Skjálfandi Bay, Iceland

Anthropogenic activity has contributed to increased extinction rates, creating a need to monitor and conserve vulnerable species. Understanding the distribution and habitat preference of threatened species can identify crucial habitats, for which protection can improve the population size numbers. Here, we investigate the habitat preference of the common minke whale, a rapidly declining yet understudied cetacean species. We analysed minke whale sightings over time and in relation to environmental factors (depth, sea surface temperature, sediment, chlorophyll), based on long-term monitoring data from Skjálfandi Bay in the northeast of Iceland. We found minke whales have a preference for water depth between 9-70m, and water temperature of either colder than 6°C or warmer than 9°C. Shallow depth was a strong predictor of minke whale presence, which matched sandeel distribution. Sandeels require shallow depths for spawning and overwinter burrowing, and the match between minke whale depth presence and sandeel habitat is in good agreement with sandeels being an important minke whale food source. Although the relationship between minke whale presence and sea surface temperature is weak, it also matched sandeel distribution. We also detected a decline in minke whale population size over the study period (2009-2018). The population decline observed here is consistent with the population trend estimated for the Icelandic population. We suggest that the habitat preferences identified here should be considered for conservation recommendations and minimising disturbance in the identified, crucial feeding areas.

Fast-growing species shape the evolution of reef corals

Ecological interactions are ubiquitous on tropical coral reefs, where sessile organisms coexist in limited space. Within these high-diversity systems, reef-building scleractinian corals form an intricate interaction network. The role of biotic interactions among reef corals is well established on ecological timescales. However, its potential effect on macroevolutionary patterns remains unclear. By analysing the rich fossil record of Scleractinia, we show that reef coral biodiversity experienced marked evolutionary rate shifts in the last 3 million years, possibly driven by biotic interactions. Our models suggest that there was an overwhelming effect of staghorn corals (family Acroporidae) on the fossil diversity trajectories of other coral groups. Staghorn corals showed an unparalleled spike in diversification during the Pleistocene. But surprisingly, their expansion was linked with increases in both extinction and speciation rates in other coral families, driving a nine-fold increase in lineage turnover. These results reveal a double-edged effect of diversity dependency on reef evolution. Given their fast growth, staghorn corals may have increased extinction rates via competitive interactions, while promoting speciation through their role as ecosystem engineers. This suggests that recent widespread human-mediated reductions in staghorn coral cover, may be disrupting the key macroevolutionary processes that established modern coral reef ecosystems.

Regional landscape change triggered by Andean uplift: The extinction of Sparassodonta (Mammalia, Metatheria) in South America

Sparassodonta, a Metatherian monophyletic group, was the main mammalian carnivore predator clade in South America from the Paleogene to the Early Pliocene (c. 66–3.5 Ma). However, there is still no consensus on the causes of their demise. Here, we use the fossil record and Bayesian diversification models to infer the origination and extinction rates for Sparassodonta. Then, we evaluate if their demise can be attributed to global temperature changes, Andean uplift, biotic interactions with their competitor and prey clades, and body mass evolution. That is biotic aspects in the context of the Red Queen model, abiotic aspects in the context of the Court Jester model, and an intrinsic lineage attribute. Our results show that this lineage is characterized by a positive near-zero net diversification rate indicating that the clade maintained a relatively low but stable diversity until the Middle Miocene when an increase in extinction rate drove them to decline and eventual extinction. Moreover, our results support the idea that a drastic regional landscape change triggered by the Andean uplift process affected their diversification dynamics, eventually driving them to extinction. These environmental changes could explicitly affect Sparassodonta lineages due to their ever-present vulnerability to extinction by near-zero net diversification rate and their highly specialized ecology that could have constrained adaptation to new South American landscapes. • We evaluate biotic and abiotic hypotheses to understand the causes of the Sparassodonta extinction. • We estimate the Sparassodonta macroevolutionary trajectories and evaluate their relationship with biotic and abiotic factors. • We find that Sparassodonts did not succumb to biotic interactions (competition and predation) or body size evolution. • The Sparassodonta decline resulted from the regional landscape changes during the Miocene associated with Andean uplift.

Longer daylengths associated with poleward range shifts accelerate aphid extinction by parasitoid wasps

Abstract Climate change is causing the poleward range‐shift of many species, with consequent modifications to daylight regimes and potential impacts on light‐cycle activity patterns and ecological interactions. Day‐active parasitoids experiencing longer summer days associated with a poleward range shift display increased attack rates on their aphid hosts and have higher lifetime fecundity. Theory consequently predicts that with increasing photoperiod, host–parasitoid interactions would become less stable with more variable population densities and increased extinction probability. To test this prediction empirically, we conducted a multigenerational aphid‐parasitoid microcosm experiment in which we followed population dynamics under 14 and 18 h daylight treatments. As predicted, we found an increased extinction rate of both aphids and parasitoids with longer daylengths. The long‐day treatments also exhibited higher temporal variation in parasitoid numbers and increased cumulative parasitoid population size, consistent with the prediction that increased aphid extinctions are due to increased parasitoid attack rates. Our results demonstrate that light regime can affect the dynamics of interacting species and potentially limit the co‐existence of hosts and parasitoids, as well as other trophically interacting taxa where activity patterns are dependent on the light regime. This highlights the importance of the rarely considered effect of changing daylight conditions associated with climate change–driven range shifts, which could limit poleward range shifts due to changing ecological interactions.

Optogenetic stimulation of striatal patches modifies habit formation and inhibits dopamine release

Habits are inflexible behaviors that develop after extensive repetition, and overreliance on habits is a hallmark of many pathological states. The striatum is involved in the transition from flexible to inflexible responding, and interspersed throughout the striatum are patches, or striosomes, which make up ~15% of the volume of the striatum relative to the surrounding matrix compartment. Previous studies have suggested that patches are necessary for normal habit formation, but it remains unknown exactly how patches contribute to habit formation and expression. Here, using optogenetics, we stimulated striatal patches in Sepw1-NP67 mice during variable interval training (VI60), which is used to establish habitual responding. We found that activation of patches at reward retrieval resulted in elevated responding during VI60 training by modifying the pattern of head entry and pressing. Further, this optogenetic manipulation reduced subsequent responding following reinforcer devaluation, suggesting modified habit formation. However, patch stimulation did not generally increase extinction rates during a subsequent extinction probe, but did result in a small ‘extinction burst’, further suggesting goal-directed behavior. On the other hand, this manipulation had no effect in omission trials, where mice had to withhold responses to obtain rewards. Finally, we utilized fast-scan cyclic voltammetry to investigate how patch activation modifies evoked striatal dopamine release and found that optogenetic activation of patch projections to the substantia nigra pars compacta (SNc) is sufficient to suppress dopamine release in the dorsal striatum. Overall, this work provides novel insight into the role of the patch compartment in habit formation, and provides a potential mechanism for how patches modify habitual behavior by exerting control over dopamine signaling.

Parthenogenesis is self-destructive for scaled reptiles.

Parthenogenesis is rare in nature. With 39 described true parthenogens, scaled reptiles (Squamata) are the only vertebrates that evolved this reproductive strategy. Parthenogenesis is ecologically advantageous in the short term, but the young age and rarity of parthenogenetic species indicate it is less advantageous in the long term. This suggests parthenogenesis is self-destructive: it arises often but is lost due to increased extinction rates, high rates of reversal or both. However, this role of parthenogenesis as a self-destructive trait remains unknown. We used a phylogeny of Squamata (5388 species), tree metrics, null simulations and macroevolutionary scenarios of trait diversification to address the factors that best explain the rarity of parthenogenetic species. We show that parthenogenesis can be considered as self-destructive, with high extinction rates mainly responsible for its rarity in nature. Since these parthenogenetic species occur, this trait should be ecologically relevant in the short term.

Historical diversification and biogeography of the endemic southern African dung beetle genus, Epirinus (Scarabaeidae: Scarabaeinae)

Abstract The role of the geological uplift and climatic changes during the late Cenozoic on the species diversification of southern African dung beetles is not fully understood. Therefore, we use a divergence-time-estimated phylogeny, macroevolutionary analyses and ecological niche modelling under different climatic scenarios to investigate diversification of the endemic southern African genus, Epirinus. We predict the ancestral range and vegetation type occupied by Epirinus and how late Cenozoic climatic fluctuations and resulting vegetation changes affected speciation and extinction of Epirinus species. Our results suggest that the genus originated in forest with radiation into three geographical centres: (a) north-east escarpment forest and highland grassland; (b) south-east forest; and (c) south-west lowlands to north-east uplands in open vegetation. Reduced speciation rates in the mid-Miocene and increased extinction rates during the drier and cooler Plio-Pleistocene coincide with the replacement of forest by grassland or savanna in southern Africa. The drier climate in southern Africa may have driven extensive contraction of shaded vegetation, forcing an adaptation of forest inhabitants to upland grassland environments, or driving Epirinus species to extinction. Our study supports hypothesis of climatically driven diversification of Epirinus whereas ecological niche modelling across different geological periods suggest that the south-east and, to a lesser extent, the west coast of South Africa as stable areas.

The Late Capitanian Mass Extinction of Terrestrial Vertebrates in the Karoo Basin of South Africa

The Beaufort Group of the main Karoo Basin of South Africa records two major extinction events of terrestrial vertebrates in the late Palaeozoic. The oldest of these has been dated to the late Capitanian and is characterized by the extinction of dinocephalian therapsids and bradysaurian pareiasaurs near the top of Tapinocephalus Assemblage Zone. Faunal turnover associated with the extinction of dinocephalians is evident in vertebrate faunas from elsewhere in Pangaea but it can be best studied in the Karoo Basin, where exposures of the upper Abrahamskraal and lower Teekloof formations allow continuous sampling across the whole extinction interval. Here we present field data for several sections spanning the Capitanian extinction interval in the southwestern Karoo and discuss recent work to establish its timing, severity, and causes. A large collections database informed by fieldwork demonstrates an increase in extinction rates associated with ecological instability that approach that of the end-Permian mass extinction, and shows significant turnover followed by a period of low diversity. Extinctions and recovery appear phased and show similarities to diversity patterns reported for the end-Permian mass extinction higher in the Beaufort sequence. In the Karoo, the late Capitanian mass extinction coincides with volcanism in the Emeishan Large Igneous Province and may have been partly driven by short-term aridification, but clear causal mechanisms and robust links to global environmental phenomena remain elusive.

Long‐term effects of colonization–extinction dynamics of generalist versus specialist wood‐decaying fungi

Abstract Long‐term metapopulation persistence is mediated by the dynamics of colonization and extinction. To understand and predict future species occupancy in changing landscapes, we must account for the dynamic rates that shape the occupancy and disentangle their dependence on environmental conditions. Specialist and generalist species may differ in their dynamics in systematic ways. Using an extensive, large‐scale repeat survey dataset for wood‐decaying fungi, we fitted dynamic metapopulation models for ten species, ranging from generalists to specialists with differing resource requirements. We first estimated base rates of colonization and extinction and tested their relationships to species' degree of specialization. We then tested for effects of local and landscape scale variables on the colonization and extinction rates. Finally, using the fitted models and a scenario of future forest development we projected future colonization–extinction dynamics over 100 years to test for differences in species occupancies between production stands and set‐aside stands. Our study revealed a striking pattern of decreasing colonization rates with increasing degree of specialization across species, along with concomitantly increasing extinction rates. Strong sensitivity of colonization probabilities to local habitat quality (dead wood volume and stand age) in specialist but not generalist species constrained the regional occupancy of specialists, especially in production forest. We found evidence for short‐range dispersal limitation in two specialists, but no effect of our measure for landscape‐scale connectivity on colonization rates. Simulations of future metapopulation dynamics resulted in decreasing and lower final occupancy in production forest than in set‐asides, especially of specialist species. In set‐aside stands, however, specialists increased over time to relatively high occupancies. Synthesis. Colonization–extinction dynamics of wood‐decaying fungi varied with species' degree of specialization. Increasing specialization was associated with increasing sensitivity of colonization rates to habitat conditions, and partly local connectivity, as well as with increasing extinction rates. Low landscape‐scale occupancies of specialist as compared to generalist wood‐decaying fungi are thus maintained by a combination of lower colonization rates, particularly in production forest, and higher extinction rates.

Multiple lineages of hyper‐diverse Zopheridae beetles survived the New Zealand Oligocene Drowning

AbstractAimDuring the late Oligocene (23 mya) the New Zealand landmass was reduced to approximately 18% of its current area. It has been hypothesized that this event, known as the Oligocene Drowning, caused population bottlenecking and mass extinction. Using phylogenetic methods, we examine the effect of this and other environmental events on the hyper‐diverse Zopheridae beetles (162 morphospecies), which largely inhabit leaf litter and dead wood.LocationNew Zealand.TaxonZopheridae, Coleoptera.MethodsHere we use a fossil‐calibrated phylogenetic tree estimated from mitochondrial cytochrome c oxidase subunit I and nuclear large subunit rRNA genes to identify monophyletic New Zealand zopherid lineages and date the age of these lineages. We used Bayesian diversification models (compound Poisson process on mass extinction times) to test the hypothesis that the New Zealand zopherids underwent a mass extinction in the late Oligocene followed by an increase in speciation rate in the Miocene. We also used these data to estimate the age of these lineages in New Zealand.ResultsWe demonstrate that 15–20 zopherid lineages survived the Oligocene Drowning depending on the calibration scheme. Of these lineages from 3 to 11 have posterior intervals that encompass the rifting of New Zealand from Gondwana in the late Cretaceous, again depending on the calibration scheme. The diversification model shows no evidence of an increase in extinction rate during the Oligocene Drowning or during any other period since the Cretaceous. Furthermore, rather than recovering an increase in speciation rate during the Miocene and Pliocene, due to environmental changes, we instead recovered a large drop in the speciation rate during this time.Main conclusionsThe New Zealand zopherid fauna is a combination of lineages, some of which may have existed on New Zealand since the rifting from Gondwana and other more recent arrivals. The late Oligocene reduction in land area was insufficient to cause a mass extinction in the Zopheridae. This suggests the amount of emergent land was great enough to support a diverse invertebrate fauna. Our study demonstrates the different biogeographic patterns evident in cryptic, hyper‐diverse, and poorly dispersing invertebrate species relative to more mobile plants and animals.

Lots of loss with little scrutiny: The attrition of habitat critical for threatened species in Australia

AbstractAustralia has one of the worst extinction rates of any nation, yet there has been little assessment of the effect of its flagship environmental legislation, the Environment Protection and Biodiversity Conservation Act 1999 (EPBC Act), to prevent species extinction. By coupling remotely sensed forest and woodland data with the distributions of 1,638 terrestrial threatened species, terrestrial migratory species, and threatened ecological communities, we quantified the loss of potential habitat and communities since the EPBC Act came into force in 2000. We found that over 7.7 million ha of potential habitat and communities were cleared in the period 2000–2017. Of this clearing, over 93% was not referred to the Federal Government for assessment, meaning the loss was not scrutinized under the EPBC Act. While 1,390 (84%) species suffered loss, Mount Cooper striped skink, Keighery's macarthuria, and Southern black‐throated finch lost 25, 23, and 10% of potential habitat, respectively. Iconic Australian species, such as koala, also lost ~1 million ha (2.3%) of potential habitat. Our analysis showed that the EPBC Act is ineffective at protecting potential habitat for terrestrial threatened species, terrestrial migratory species, or threatened ecological communities. We recommend that when scientifically determinable, critical habitat is demarcated for listed species and communities, which provides absolute protection that is enforced, monitored, and investigated by the regulator. Without a fundamental change in how environmental law is enforced, Australia faces an increasing extinction rate.

Estimating Diversity Through Time Using Molecular Phylogenies: Old and Species-Poor Frog Families are the Remnants of a Diverse Past.

Estimating how the number of species in a given group varied in the deep past is of key interest to evolutionary biologists. However, current phylogenetic approaches for obtaining such estimates have limitations, such as providing unrealistic diversity estimates at the origin of the group. Here, we develop a robust probabilistic approach for estimating diversity through time curves and uncertainty around these estimates from phylogenetic data. We show with simulations that under various realistic scenarios of diversification, this approach performs better than previously proposed approaches. We also characterize the effect of tree size and undersampling on the performance of the approach. We apply our method to understand patterns of species diversity in anurans (frogs and toads). We find that Archaeobatrachia-a species-poor group of old frog clades often found in temperate regions-formerly had much higher diversity and net diversification rate, but the group declined in diversity as younger, nested clades diversified. This diversity decline seems to be linked to a decline in speciation rate rather than an increase in extinction rate. Our approach, implemented in the R package RPANDA, should be useful for evolutionary biologists interested in understanding how past diversity dynamics have shaped present-day diversity. It could also be useful in other contexts, such as for analyzing clade-clade competitive effects or the effect of species richness on phenotypic divergence.

The Effects of Interaction between Climate Change and Land-Use/Cover Change on Biodiversity-Related Ecosystem Services.

Climate change and land‐use/cover change (LUCC) are two major types of global environmental change. They are increasingly challenging the main objectives of ecosystem management, which are to provide ecosystem services sustainably to society and maintain biodiversity. However, a comprehensive understanding of how climate–land‐use change affects these primary goals of ecosystem management is still lacking. Here, a global literature review on the impacts of climate change and LUCC on ecosystem services related to biodiversity is presented. In this review, possible ecological responses at species, community, and ecosystem levels, and the effects of interaction mechanisms between climate change and LUCC on biodiversity‐related ecosystem services are identified. The results show possible effects on species facing climate change challenges through affecting distribution/range shifts, interspecific relations, richness, and abundance, and the impacts on biodiversity through increasing extinction rates, nutrient deposition, and habitat fragmentation under LUCC. Climate change may hinder the ability of species to deal with LUCC, and in turn LUCC could reduce resilience to climate change. Understanding of these interactions is necessary to address the increasing pressure on sustainable provisioning of ecosystem services under different climate and land‐use scenarios in the future.

An analysis of the impacts of Cretaceous oceanic anoxic events on global molluscan diversity dynamics

AbstractOceanic anoxic events (OAEs) are contemporaneous with 11 of the 18 largest Phanerozoic extinction events, but the magnitude and selectivity of their paleoecological impact remains disputed. OAEs are associated with abrupt, rapid warming and increased CO2flux to the atmosphere; thus, insights from this study may clarify the impact of current anthropogenic climate change on the biosphere. We investigated the influence of the Late Cretaceous Bonarelli event (OAE2; Cenomanian/Turonian stage boundary; ~94 Ma) on generic- and species-level molluscan diversity, extinction rates, and ecological turnover. Cenomanian/Turonian results were compared with changes across all Cretaceous stage boundaries, some of which are coincident with less severe OAEs. We found increased generic turnover, but not species-level turnover, associated with several Cretaceous OAEs. The absence of a species-level pattern may reflect species occurrence data that are too temporally coarse to robustly detect patterns. Five hypotheses of ecological selectivity relating anoxia to survivorship were tested across stage boundaries with respect to faunality, mobility, and diet using generalized linear models. Interestingly, benthic taxa were consistently selected against throughout the Cretaceous regardless of the presence or absence of OAEs. These results suggest that: (1) the Cenomanian/Turonian boundary (OAE2) was associated with a decline in molluscan diversity and increase in extinction rate that were significantly more severe than Cretaceous background levels; and (2) no differential ecological selectivity was associated with OAE-related diversity declines among the variables tested here.

Ecological drift and competitive interactions predict unique patterns in temporal fluctuations of population size.

Recent studies have highlighted the importance of higher-order competitive interactions in stabilizing population dynamics in multi-species communities. But how does the structure of competitive hierarchies affect population dynamics and extinction processes? We tackled this important question by using spatially explicit simulations of ecological drift (10 species in a homogeneous landscape of 64 patches) in which birth rates were influenced by interspecific competition. Specifically, we examined how transitive (linear pecking orders) and intransitive (pecking orders with loops) competitive hierarchies affected extinction rates and population dynamics in simulated communities through time. In comparison to a pure neutral model, an ecological drift model including transitive competition increased extinction rates, caused synchronous density-dependent population fluctuations, and generated a white-noise distribution of population sizes. In contrast, the drift model with intransitive competitive interactions decreased extinctions rates, caused asynchronous (compensatory) density-dependent population fluctuations, and generated a brown noise distribution of population sizes. We also explored the effect on community stability of more complex patterns of competitive interactions in which pairwise competitive relationships were assigned probabilistically. These probabilistic competition models also generated density-dependent trajectories and a brown noise distribution of population sizes. However, extinction rates and the degree of population synchrony were comparable to those observed in purely neutral communities. Collectively, our results confirm that intransitive competition has a strong and stabilizing effect on local populations in species-poor communities. This effect wanes with increasing species richness. Empirical assemblages characterized by brown spectral noise, density-dependent regulation, and asynchronous (compensatory) population fluctuations may indicate a signature of intransitive competitive interactions.

How survival curves affect populations' vulnerability to climate change.

Human activities are exposing organisms not only to direct threats (e.g. habitat loss) but also to indirect environmental pressures such as climate change, which involves not just directional global warming but also increasing climatic variability. Such changes will impact whole communities of organisms and the possible effects on population dynamics have raised concerns about increased extinction rates. Conservation-minded approaches to extinction risk vary from range shifts predicted by climate envelope models with no population dynamics to population viability analyses that ignore environmental variability altogether. Our modelling study shows that these extremes are modelling responses to a spectrum of environmental sensitivity that organisms may exhibit. We show how the survival curve plays a major role in how environmental variability leads to population fluctuations. While it is often supposed that low-fecundity organisms (those with high parental investment) will be the most vulnerable to climate change, it is those with high fecundity (low parental investment) that are likely to be more sensitive to such changes. We also find that abundance variations in high fecundity populations is driven primarily by fluctuations in the survival of early life stages, the more so if those environmental changes are autocorrelated in time. We show which types of conservation actions are most appropriate for a number of real populations. While the most effective conservation actions for organisms of low fecundity is to avoid killing them, for populations with high fecundity (and low parental investment), our study suggests conservation should focus more on protecting early life stages from hostile environments.

How Well Can We Estimate Diversity Dynamics for Clades in Diversity Decline?

The fossil record shows that the vast majority of all species that ever existed are extinct and that most lineages go through an expansion and decline in diversity. However, macroevolutionary analyses based upon molecular phylogenies have difficulty inferring extinction dynamics, raising questions about whether the neontological record can contribute to an understanding of the decline phenomenon. Two recently developed diversification methods for molecular phylogenies (RPANDA and BAMM) incorporate models that theoretically have the capacity to capture decline dynamics by allowing extinction to be higher than speciation. However, the performance of these frameworks over a wide range of decline scenarios has not been studied. Here, we investigate the behavior of these methods under decline scenarios caused by decreasing speciation and increasing extinction through time on simulated trees at fixed intervals over diversity trajectories with expansion and decline phases. We also compared method performance over a comprehensive data set of 214 empirical trees. Our results show that both methods perform equally well when varying speciation rates control decline. When decline was only caused by an increase in extinction rates both methods wrongly assign the variation in net diversification to a drop in speciation, even though the positive gamma values of those trees would suggest otherwise. We also found a tendency for RPANDA to favor increasing extinction and BAMM to favor decreasing speciation as the most common cause of decline in empirical trees. Overall our results shed light on the limitations of both methods, encouraging researchers to carefully interpret the results from diversification studies.

Plant traits and population characteristics predict extinctions in a long-term survey of Mediterranean annual plants

Global and local environmental changes lead to frequent plant extinctions many of which occur in man-made habitats such as agricultural fields. Plant traits and site conditions modify risks of extinction, but strength and sense of their effect are not known yet. Here, we present a long-term survey of population sizes for Mediterranean annual plants that we revisited 20 years after their first record to evaluate climate, population size, traits and habitat requirements as drivers of local extinctions. Small populations had an increased probability of extinction in our data-set. Our analyses revealed that seed production and survival of seeds in the soil seed bank decreased extinction rate, whereas plant size increased extinction probability. Mean annual temperature increased extinction rates of annual plants in cereal fields. We discuss these effects as a response to recent and ongoing habitat changes, and discuss how traits may be used to guide conservation practices in the face of local extinctions.