Global Patterns and Drivers of Avian Extinctions at the Species and Subspecies Level

Birds have long fascinated scientists and travellers, so their distribution and abundance through time have been better documented than those of other organisms. Many bird species are known to have gone extinct, but information on subspecies extinctions has never been synthesised comprehensively. We reviewed the timing, spatial patterns, trends and causes of avian extinctions on a global scale, identifying 279 ultrataxa (141 monotypic species and 138 subspecies of polytypic species) that have gone extinct since 1500. Species extinctions peaked in the early 20^th century, then fell until the mid 20^th century, and have subsequently accelerated. However, extinctions of ultrataxa peaked in the second half of the 20^th century. This trend reflects a consistent decline in the rate of extinctions on islands since the beginning of the 20^th century, but an acceleration in the extinction rate on continents. Most losses (78.7% of species and 63.0% of subspecies) occurred on oceanic islands. Geographic foci of extinctions include the Hawaiian Islands (36 taxa), mainland Australia and islands (29 taxa), the Mascarene Islands (27 taxa), New Zealand (22 taxa) and French Polynesia (19 taxa). The major proximate drivers of extinction for both species and subspecies are invasive alien species (58.2% and 50.7% of species and subspecies, respectively), hunting (52.4% and 18.8%) and agriculture, including non-timber crops and livestock farming (14.9% and 31.9%). In general, the distribution and drivers of subspecific extinctions are similar to those for species extinctions. However, our finding that, when subspecies are considered, the extinction rate has accelerated in recent decades is both novel and alarming.     

Spatial scaling of extinction rates: Theory and data reveal nonlinearity and a major upscaling and downscaling challenge

Aim

Biodiversity loss is a key component of biodiversity change and can impact ecosystem services. However, estimation of the loss has focused mostly on per‐species extinction rates measured over a limited number of spatial scales, with little theory linking small‐scale extirpations to global extinctions. Here, we provide such a link by introducing the relationship between area and the number of extinctions (number of extinctions–area relationship; NxAR) and between area and the proportion of extinct species (proportion of extinctions–area relationship; PxAR). Unlike static patterns, such as the species–area relationship, NxAR and PxAR represent spatial scaling of a dynamic process. We show theoretical and empirical forms of these relationships and we discuss their role in perception and estimation of the current extinction crisis.

Location

U.S.A., Europe, Czech Republic and Barro Colorado Island (Panama).

Time period

1500–2009.

Major taxa studied

Vascular plants, birds, butterflies and trees.

Methods

We derived the expected forms of NxAR and PxAR from several theoretical frameworks, including the theory of island biogeography, neutral models and species–area relationships. We constructed NxAR and PxAR from five empirical datasets collected over a range of spatial and temporal scales.

Results

Although increasing PxAR is theoretically possible, empirical data generally support a decreasing PxAR; the proportion of extinct species decreases with area. In contrast, both theory and data revealed complex relationships between numbers of extinctions and area (NxAR), including nonlinear, unimodal and U‐shaped relationships, depending on region, taxon and temporal scale.

Main conclusions

The wealth of forms of NxAR and PxAR explains why biodiversity change appears scale dependent. Furthermore, the complex scale dependence of NxAR and PxAR means that global extinctions indicate little about local extirpations, and vice versa. Hence, effort should be made to understand and report extinction rates as a scale‐dependent problem. In this effort, estimation of scaling relationships such as NxAR and PxAR should be central.     

A theoretical quantitative genetic study of negative ecological interactions and extinction times in changing environments

Background  

Rapid human-induced changes in the environment at local, regional and global scales appear to be contributing to population declines and extinctions, resulting in an unprecedented biodiversity crisis. Although in the short term populations can respond ecologically to environmental alterations, in the face of persistent change populations must evolve or become extinct. Existing models of evolution and extinction in changing environments focus only on single species, even though the dynamics of extinction almost certainly depend upon the nature of species interactions.     

High seedling relative growth rate and specific leaf area are traits of invasive species: phylogenetically independent contrasts of woody angiosperms

Understanding causal factors of exotic species invasions is important not only for prevention and prioritizing control efforts, but also for providing valuable insights into the underlying biology of contrasting life-history strategies. In seedling growth analyses, invasive woody species were compared with less-invasive woody species commonly cultivated in California using phylogenetically corrected procedures (12 phylogenetically independent contrasts). Invasive species were hypothesized to have higher seedling relative growth rates (RGRs) and specific leaf areas (SLAs) than did related less-invasive species. In phylogenetically independent contrasts conducted among taxa within families, high seedling RGRs and SLAs have significant positive associations with woody plant invasiveness. For contrasts containing species invasive in mediterranean regions, invasive species had significantly larger root biomass allocation than did less-invasive species. Optimization of fast seedling growth (high RGR) associated with opportunistic resource acquisition (high SLA) and increased root allocation to survive summer drought may be critical for the success of plant invaders in regions with mediterranean climates.     

The ghosts of mammals past: biological and geographical patterns of global mammalian extinction across the Holocene

Although the recent historical period is usually treated as a temporal base-line for understanding patterns of mammal extinction, mammalian biodiversity loss has also taken place throughout the Late Quaternary. We explore the spatial, taxonomic and phylogenetic patterns of 241 mammal species extinctions known to have occurred during the Holocene up to the present day. To assess whether our understanding of mammalian threat processes has been affected by excluding these taxa, we incorporate extinct species data into analyses of the impact of body mass on extinction risk. We find that Holocene extinctions have been phylogenetically and spatially concentrated in specific taxa and geographical regions, which are often not congruent with those disproportionately at risk today. Large-bodied mammals have also been more extinction-prone in most geographical regions across the Holocene. Our data support the extinction filter hypothesis, whereby regional faunas from which susceptible species have already become extinct now appear less threatened; they may also suggest that different processes are responsible for driving past and present extinctions. We also find overall incompleteness and inter-regional biases in extinction data from the recent fossil record. Although direct use of fossil data in future projections of extinction risk is therefore not straightforward, insights into extinction processes from the Holocene record are still useful in understanding mammalian threat.     

Phylogenetic patterns of colonization and extinction in experimentally assembled plant communities

Background

Evolutionary history has provided insights into the assembly and functioning of plant communities, yet patterns of phylogenetic community structure have largely been based on non-dynamic observations of natural communities. We examined phylogenetic patterns of natural colonization, extinction and biomass production in experimentally assembled communities.

Methodology/Principal Findings

We used plant community phylogenetic patterns two years after experimental diversity treatments (1, 2, 4, 8 or 32 species) were discontinued. We constructed a 5-gene molecular phylogeny and statistically compared relatedness of species that colonized or went extinct to remaining community members and patterns of aboveground productivity. Phylogenetic relatedness converged as species-poor plots were colonized and speciose plots experienced extinctions, but plots maintained more differences in composition than in phylogenetic diversity. Successful colonists tended to either be closely or distantly related to community residents. Extinctions did not exhibit any strong relatedness patterns. Finally, plots that increased in phylogenetic diversity also increased in community productivity, though this effect was inseparable from legume colonization, since these colonists tended to be phylogenetically distantly related.

Conclusions

We found that successful non-legume colonists were typically found where close relatives already existed in the sown community; in contrast, successful legume colonists (on their own long branch in the phylogeny) resulted in plots that were colonized by distant relatives. While extinctions exhibited no pattern with respect to relatedness to sown plotmates, extinction plus colonization resulted in communities that converged to similar phylogenetic diversity values, while maintaining differences in species composition.     

BIODIVERSITY RESEARCH: When is a species really extinct? Testing extinction inference from a sighting record to inform conservation assessment

Aim The global extinction of a species typically represents the end point in a series of population extinctions, during which unique evolutionary history is lost at every stage. Insight into the process of extinction can provide the means to identify species at high risk, but the number of extinctions being identified languishes far behind true totals. More proactive ways of inferring extinction from limited data are required. Location Historic sightings, collections and specimen data from Australia and Asia. Method We used a technique called optimal linear estimation to analyse the sightings record of mammal and bird species of varying ecology, life history and population demography. The mammal species chosen were all considered regionally extinct in the literature, while the bird species chosen had all been highlighted as candidates for the new IUCN Red List category flag: Critically Endangered (Possibly Extinct). Results Nine of the ten mammal species were predicted to be probably extinct, but only two with 95% certainty. Seven of the ten bird species were predicted to be probably extinct, four with 95% certainty. Main conclusions Superficially, determining whether a species is extinct might seem a simple task, whereby we either find a species extant, or it is extinct. In reality, however, the task is much more complex. Techniques such as optimal linear estimation, in combination with other data sources, and knowledge of recording effort, may prove useful in inferring extinction across a variety of taxa but should not be used in isolation.     

Reductions in connectivity and habitat quality drive local extinctions in a plant diversity hotspot

It is well documented that habitat loss is a major cause of biodiversity decline. However, the roles of the different aspects of habitat loss in local extinctions are less understood. Anthropogenic destruction of an area of habitat causes immediate local extinction but subsequently three additional gradual drivers influence the likelihood of delayed extinction: decreased habitat patch size, lower connectivity and habitat deterioration. We investigated the role of these drivers in local extinctions of 82 declining species in a UK biodiversity hotspot. We combined a unique set of ≈ 7000 vegetation surveys and habitat maps from the 1930s with contemporary species’ occurrences. We extrapolated from these surveys to the whole 2500‐km² study area using habitat suitability surfaces. The strengths of drivers in explaining local extinctions over this 70 yr period were determined by contrasting connectivity, patch size and habitat quality loss for locations at which a species went extinct and those with persisting occurrences. Species’ occurrences declined on average by 60%, with half of local extinctions attributable to immediate habitat loss and half to the gradual processes causing delayed extinctions. On average, locations where a species persisted had a 73% higher contemporary connectivity than those suffering extinctions, but showed no differences in historical connectivity. Furthermore, locations with extinctions experienced a 37% greater decline in suitability associated with changes in habitat type. The strength of the drivers and the proportion of extinctions depended on the species’ habitat specialism, but were affected only minimally by life‐history characteristics. In conclusion, we identified a hierarchy of drivers influencing local extinction: with connectivity loss being the strongest, suitability change being moderately important, but changes in habitat patch size having only weak effects. We suggest conservation efforts could be most effective by strengthening connectivity along with reducing habitat deterioration, which would benefit a wide range of species.     

Functional and historical drivers of leaf shape evolution in palms (Arecaceae)

Aim

Leaves display a remarkable variety of shapes, each with potential ecological advantages in specific climates. While the relations between leaf shape and either climate or height have been relatively well studied in eudicots, the macroecological drivers of shape remain poorly known in monocots. Here, we investigated the associations between climate and plant height with the evolution of leaf shape in a clade with high species and morphological diversity.

Location

Global.

Time period

Cretaceous to contemporary.

Major taxa studied

Palms (Arecaceae).

Methods

We apply a Bayesian phylogenetic mixed model to test for associations between climate and leaf shape (all – entire-leaved, pinnate-dissected, palmate-dissected and costapalmate). We further reconstruct the ancestral leaf shape using multistate speciation and extinction models and compare the frequency of shapes with global temperatures through time.

Results

We find that plant height associates with dissected leaves and that annual precipitation associates with pinnate shapes. The ancestral leaf shape is unclear, but early diversification was dominated by pinnate-dissected palms, which has remained the most species-rich form of leaves throughout palm history.

Main Conclusions

Palms that are tall and live in humid regions are more likely to have pinnate leaves. Through geological time scales, temperature did not play an obvious role in determining leaf shapes. This study contributes to our understanding of how the diversity of leaf shapes is linked to biological and climatic factors.     

Characteristics of Pleistocene megafauna extinctions in Southeast Asia

The extinction of large-bodied taxa from the Pleistocene in Southeast Asia is examined. Although the chronological resolution of these extinctions is poor, and number of excavations in the region relatively few, broad characteristics of these extinctions can be described. Many taxa which became extinct appear to have been endemic to regions within Southeast Asia, while some taxa which experienced extinction or severe range reduction occurred in several regions. Members of the latter group include proboscideans (Stegodon and Palaeloxodon), the pygmy hippopotamus (Hexaprotodon), the orangutan (Pongo), hyenas (Crocuta and Hyaena), the giant panda (Ailuropoda), tapirs (Tapirus and Megatapirus), rhinoceroses (Rhinoceros), and the giant Asian ape Gigantopithecus. The loss of these species cannot be assigned to a single cause. Rather their disappearance is likely tied to both climatic and human agents. Unlike other regions which experienced megafauna extinctions, eustatic changes in sea level in Southeast Asia seems to have been an important factor.     

Pattern of functional extinctions in ecological networks with a variety of interaction types

There is a strong trend of declining populations in many species of both animals and plants. Dwindling numbers of species can eventually lead to their functional extinction. Functional, or ecological, extinction occurs when a species becomes too rare to fulfill its ecological, interactive role in the ecosystem, leading to true (numerical) extinction of other depending species. Recent theoretical work on food webs suggests that the frequency of functional extinction might be surprisingly high. However, little is known about the risk of functional species extinctions in networks with other types of interactions than trophic ones. Here, we explore the frequency of functional extinctions in model ecological networks having different proportions of antagonistic and mutualistic links. Furthermore, we investigate the topological relationship between functionally and numerically extinct species. We find that (1) the frequency of functional extinctions is higher in networks containing a mixture of antagonistic and mutualistic interactions than in networks with only one type of interaction, (2) increased mortality rate of species having both mutualistic and antagonistic links is more likely to lead to extinction of another species than to extinction of the species itself compared to species having only mutualistic or antagonistic links, and (3) trophic distance (shortest path) between functionally and numerically extinct species is, on average, longer than one, indicating the importance of indirect effects. These results generalize the findings of an earlier study on food webs, demonstrating the potential importance of functional extinction in a variety of ecological network types.     

Herbarium records do not predict rediscovery of presumed nationally extinct species

Rediscoveries of species previously thought to be extinct present a dilemma to conservation biology. On one hand, such instances offer the chance to change the course of events away from one that would have led to extinctions. On the other hand, public support for conservation may wane if scientists are frequently seen to overstate and prematurely declare extinctions. Recent studies have adopted a probabilistic approach to infer extinction, using sightings or collections and statistical models to calculate the chance that a species may still be extant. We conduct the first broad-scale test of such models using a recently compiled national red list and national herbarium collection records, including collections of presumed nationally extinct species made after the red list publication, which constitute “rediscoveries”. There was little evidence that the probabilities calculated by these models were associated with rediscoveries over a 3.5-year period. Current probabilistic models of extinction using sighting records could hence be inadequate for use with most natural history collection data.     

The form of the curves: a direct evaluation of MacArthur & Wilson's classic theory

1. We calculate the yearly numbers of bird species immigrating to – and becoming extinct on – 13 small islands of the British Isles, using a long and relatively complete data record.
2. We estimate the size of the colonist pool for each island using four methods.
3. We assume that immigrations and extinctions are distributed binomially, and use a maximum likelihood method to fit concave immigration and extinction functions to the data, utilizing all four species pool estimates.
4. Extinction rates increase significantly and consistently with increasing numbers of breeding species on each island. For nine of the 13 islands the extinction functions are significantly concave.
5. Immigration rates decrease consistently with increasing numbers of breeding species on each island. Seven islands have significantly concave immigration functions.
6. Immigration rates and extinction rates decline consistently, but not significantly, with island distance and island size, respectively. The number of breeding species does not always reflect the number of species likely to have reached an island. Moreover, some species may choose not to breed when their chance of extinction is high. These factors, plus the modest range of island areas and distances in our database, reduce our chances of finding the theoretically predicted effects of area and distance on extinction and immigration rates.     

Introductions do not compensate for functional and phylogenetic losses following extinctions in insular bird assemblages

The ratio of species extinctions to introductions has been comparable for many insular assemblages, suggesting that introductions could have ‘compensated’ for extinctions. However, the capacity for introduced species to replace ecological roles and evolutionary history lost following extinction is unclear. We investigated changes in bird functional and phylogenetic diversity in the wake of extinctions and introductions across a sample of 32 islands worldwide. We found that extinct and introduced species have comparable functional and phylogenetic alpha diversity. However, this was distributed at different positions in functional space and in the phylogeny, indicating a ‘false compensation’. Introduced and extinct species did not have equivalent functional roles nor belong to similar lineages. This makes it unlikely that novel island biotas composed of introduced taxa will be able to maintain ecological roles and represent the evolutionary histories of pre‐disturbance assemblages and highlights the importance of evaluating changes in alpha and beta diversity concurrently.     

Body length of bony fishes was not a selective factor during the biggest mass extinction of all time

The Permo‐Triassic mass extinction devastated life on land and in the sea, but it is not clear why some species survived and others went extinct. One explanation is that lineage loss during mass extinctions is a random process in which luck determines which species survive. Alternatively, a phylogenetic signal in extinction may indicate a selection process operating on phenotypic traits. Large body size has often emerged as an extinction risk factor in studies of modern extinction risk, but this is not so commonly the case for mass extinctions in deep time. Here, we explore the evolution of non‐teleostean Actinopterygii (bony fishes) from the Devonian to the present day, and we concentrate on the Permo‐Triassic mass extinction. We apply a variety of time‐scaling metrics to date the phylogeny, and show that diversity peaked in the latest Permian and declined severely during the Early Triassic. In line with previous evidence, we find the phylogenetic signal of extinction increases across the mass extinction boundary: extinction of species in the earliest Triassic is more clustered across phylogeny compared to the more randomly distributed extinction signal in the late Permian. However, body length plays no role in differential survival or extinction of taxa across the boundary. In the case of fishes, size did not determine which species survived and which went extinct, but phylogenetic signal indicates that the mass extinction was not a random field of bullets.     

Late-Quaternary megafauna extinctions have strongly reduced mammalian vegetation consumption

Aim

How much stronger would the effects of herbivorous mammals be in natural ecosystems if human-linked extinctions and extirpations had not occurred? Many mammal species have experienced range contractions, and numerous species have gone extinct in the late Quaternary, completely or in large part linked to human pressures. Therefore, herbivore consumption rates in seemingly natural ecosystems will deviate from their pre-anthropogenic state. Here, we estimate the size of this deviation.

Location

Terrestrial systems, globally.

Time period

Current.

Major taxa studied

All late-Quaternary terrestrial mammals.

Methods

We estimated and mapped vegetation consumption rate by all late-Quaternary terrestrial mammals. We did this through the estimation of natural densities and dietary needs. We mapped their consumption rate in both current ranges and present-natural ranges, that is estimated ranges in the absence of human-linked range contractions and extinctions. We compared these estimated consumption rates to current net primary productivity (NPP). We summarized the results across ecosystem types everywhere as well as for only the last remaining wilderness areas.

Results

We estimate that wild mammals consume a median of 11% of NPP (at the scale of 96.5 km × 96.5 km grid cells) in current natural areas and that this would have been much higher in the absence of extinctions and extirpations, namely 21%. Looking at the change per grid cell, the mammal losses result in a median 42% reduction in consumption rate. Importantly, we estimate very similar declines in herbivory in what are considered the last remaining wilderness areas.

Main conclusions

Our results suggest that the natural interaction of mammalian herbivores with vegetation in ecosystems across the world is strongly reduced by prehistoric and historic to recent species losses, even in the last remaining wilderness areas, likely with major effects on ecosystem structure and functioning.     

Archosauromorph extinction selectivity during the Triassic–Jurassic mass extinction

Many traits have been linked to extinction risk among modern vertebrates, including mode of life and body size. However, previous work has indicated there is little evidence that body size, or any other trait, was selective during past mass extinctions. Here, we investigate the impact of the Triassic–Jurassic mass extinction on early Archosauromorpha (basal dinosaurs, crocodylomorphs and their relatives) by focusing on body size and other life history traits. We built several new archosauromorph maximum‐likelihood supertrees, incorporating uncertainty in phylogenetic relationships. These supertrees were then employed as a framework to test whether extinction had a phylogenetic signal during the Triassic–Jurassic mass extinction, and whether species with certain traits were more or less likely to go extinct. We find evidence for phylogenetic signal in extinction, in that taxa were more likely to become extinct if a close relative also did. However, there is no correlation between extinction and body size, or any other tested trait. These conclusions add to previous findings that body size, and other traits, were not subject to selection during mass extinctions in closely‐related clades, although the phylogenetic signal in extinction indicates that selection may have acted on traits not investigated here.     

Marine influence controls plant phenological dynamics in Mediterranean Mexico

Aims To assess the role of moisture in phenological timing in the mediterranean coastal flora of Baja California, and specifically to assess the role of coastal fog and ocean-derived moisture in plant phenology. Moisture seems to be the primary driver of flowering times and durations at the arid end of the mediterranean-climate region, where rainfall is often sporadic (temperature and day length can be expected to play a much lesser role as they are not growth limiting). We aimed to understand: What factors drive climatic variation between sites? Are there general flowering patterns allowing us to identify phenological categories? Do flowering patterns vary in relation to site-specific weather? and most importantly, does maritime influence on weather affect flowering dynamics in coastal mediterranean ecosystems?Methods The southernmost extent of the California Floristic Province (in Baja California, Mexico) is a biological diversity hotspot of high endemism and conservation value, with two steep moisture gradients: rainfall (N–S) and coastal fogs (W–E), providing an ideal study system. We installed five weather stations across the moisture gradients, recording data hourly. We monitored flowering phenology in the square kilometer surrounding each weather station from 2010 to 2013. About 86 plant taxa were monitored across the five sites, every 6–8 weeks. Averaged climatic data is presented with general trends in flowering, and specific flowering syndromes were observed. Data for flowering intensity across the sites was analyzed using a principal components analysis.Important findings Data analysis demonstrates a general seasonal pattern in flowering times, but distinct differences in local weather and phenology between the five study sites. Three flowering syndromes are revealed in the flora: (i) water responders or spring bloomers, (ii) day-length responders or fall-blooming taxa and (iii) aseasonal bloomers with no seasonal affinity. The two moisture gradients are the strongest drivers of flowering times. Inland sites showed higher phenological variation than coastal sites where seasonality is dampened by ocean-derived moisture, which extends and buffers perennial plant phenology and is a probable driver of local endemism. Phenological controls vary globally with climate and geography; moisture is the primary driver of phenology in mediterranean climates and fog is an important climatic variable in coastal Mexico.     

Alien species as a driver of recent extinctions

We assessed the prevalence of alien species as a driver of recent extinctions in five major taxa (plants, amphibians, reptiles, birds and mammals), using data from the IUCN Red List. Our results show that alien species are the second most common threat associated with species that have gone completely extinct from these taxa since AD 1500. Aliens are the most common threat associated with extinctions in three of the five taxa analysed, and for vertebrate extinctions overall.     

Extinct even before scientific recognition: a remarkable radiation of helicinid snails (Helicinidae) on the Gambier Islands, French Polynesia

Recent literature abounds with reports of the decline and extinction of the endemic species of Achatinellidae and Partulidae in the Hawaiian and Society Islands, respectively, resulting from the introduction of the predatory snail Euglandina rosea. Here, we describe a previously unrecognised radiation of helicinid land snails from the Gambier Islands of French Polynesia, with up to seven species co-occurring in a single locality and up to eight species on a single island. This radiation had already become extinct (nine of ten species) several decades before the expansion of E. rosea in the Pacific, and even before the species were collected for scientific study. The Gambier Islands case study shows that massive extinctions of endemic land snails had already taken place in the nineteenth century, but have remained largely unrecognised and undocumented. Nine of the ten species are new to science and are described here almost entirely based on empty shells collected from the shell bank of the soil after the extinction had already taken place. This helicinid radiation alone increases the number of documented global mollusc extinctions by almost 2 %. Most of the species are minute and, at 1.5 mm, rank among the smallest, if not the smallest, species in the family. Several have apertural barriers and one has opercular apophyses—character states not previously documented in Pacific helicinids. Whereas the only surviving Gambier species belongs anatomically to the genus Sturanya, representative helicinid species from the Austral, Society and Cook Islands are not congeneric with it, and the generic name Nesiocina is here established for the latter taxa. It is hypothesised that the extinct Gambier species were also Nesiocina.