The origin and speciation of orchids.

Orchids constitute one of the most spectacular radiations of flowering plants. However, their origin, spread across the globe, and hotspots of speciation remain uncertain due to the lack of an up-to-date phylogeographic analysis. We present a new Orchidaceae phylogeny based on combined high-throughput and Sanger sequencing data, covering all five subfamilies, 17/22 tribes, 40/49 subtribes, 285/736 genera, and c. 7% (1921) of the 29 524 accepted species, and use it to infer geographic range evolution, diversity, and speciation patterns by adding curated geographical distributions from the World Checklist of Vascular Plants. The orchids' most recent common ancestor is inferred to have lived in Late Cretaceous Laurasia. The modern range of Apostasioideae, which comprises two genera with 16 species from India to northern Australia, is interpreted as relictual, similar to that of numerous other groups that went extinct at higher latitudes following the global climate cooling during the Oligocene. Despite their ancient origin, modern orchid species diversity mainly originated over the last 5 Ma, with the highest speciation rates in Panama and Costa Rica. These results alter our understanding of the geographic origin of orchids, previously proposed as Australian, and pinpoint Central America as a region of recent, explosive speciation.

The rate of species extinction in declining or fragmented ecological communities.

Loss of habitat can take many forms, ranging from the fragmentation of once-continuous habitat to the slow erosion of populations across continents. Usually, the harm leading to biodiversity loss is not immediately obvious: there is an extinction debt. Most modelling research of extinction debt has focussed on relatively rapid losses of habitat with species loss happening in response afterwards. In this paper, using a niche-orientated community model we compare and contrast two different mechanisms and find contrasting patterns of extinction debt. From small fragments, we typically see the rapid initial loss of many species, followed by a slower loss of species on larger timescales. When we consider slow incremental declines of population sizes, we find initially a slow rate of extinction which subsequently increases exponentially. In such cases, the delayed extinctions may go undetected initially both because the extinctions may be small relative to background randomness and because rate itself is not constant and takes time to reach its maximum.

Enhanced regional connectivity between western North American national parks will increase persistence of mammal species diversity.

Many protected areas worldwide increasingly resemble habitat isolates embedded in human-modified landscapes. However, establishing linkages among protected areas could significantly reduce species-loss rates. Here we present a novel method having broad applicability for assessing enhanced regional connectivity on persistence of mammal diversity. We combine theoretically-derived species relaxation rates for mammal communities with empirically-derived pathways. We assess the value of enhanced regional connectivity for two hypothetical networks of national parks in western North America: the Yellowstone-Glacier network and the Mount Rainier-North Cascades network. Linking the Yellowstone and Glacier park assemblages by eliminating barriers to movement in identified mammal dispersal pathways and by incorporating adjacent wilderness areas and known ungulate migratory routes into a protected area network would greatly enlarge available habitat. This would enhance medium to large mammal species persistence time by factor of 4.3, on average, or ~ 682 generations relative to individual parks. Similarly, linking Mount Rainier and North Cascades park assemblages would enhance mammal species persistence time by a factor of 4.3, on average, or ~305 generations relative to individual parks. Enhancing regional connectivity among western North America parks could serve as an important template for landscape-scale conservation in the 21st century.

SARS-CoV-2 as a Zooanthroponotic Infection: Spillbacks, Secondary Spillovers, and Their Importance.

In the midst of a persistent pandemic of a probable zoonotic origin, one needs to constantly evaluate the interplay of SARS-CoV-2 (severe acute respiratory syndrome-related coronavirus-2) with animal populations. Animals can get infected from humans, and certain species, including mink and white-tailed deer, exhibit considerable animal-to-animal transmission resulting in potential endemicity, mutation pressure, and possible secondary spillover to humans. We attempt a comprehensive review of the available data on animal species infected by SARS-CoV-2, as presented in the scientific literature and official reports of relevant organizations. We further evaluate the lessons humans should learn from mink outbreaks, white-tailed deer endemicity, zoo outbreaks, the threat for certain species conservation, the possible implication of rodents in the evolution of novel variants such as Omicron, and the potential role of pets as animal reservoirs of the virus. Finally, we outline the need for a broader approach to the pandemic and epidemics, in general, incorporating the principles of One Health and Planetary Health.

'Fly to a Safer North': Distributional Shifts of the Orchid Ophrys insectifera L. Due to Climate Change.

Numerous orchid species around the world have already been affected by the ongoing climate change, displaying phenological alterations and considerable changes to their distributions. The fly orchid (Ophrys insectifera L.) is a well-known and distinctive Ophrys species in Europe, with a broad distribution across the continent. This study explores the effects of climate change on the range of O. insectifera, using a species distribution models (SDMs) framework that encompasses different climatic models and scenarios for the near- and long-term future. The species' environmentally suitable area is projected to shift northwards (as expected) but downhill (contrary to usual expectations) in the future. In addition, an overall range contraction is predicted under all investigated combinations of climatic models and scenarios. While this is moderate overall, it includes some regions of severe loss and other areas with major gains. Specifically, O. insectifera is projected to experience major area loss in its southern reaches (the Balkans, Italy and Spain), while it will expand its northern limits to North Europe, with the UK, Scandinavia, and the Baltic countries exhibiting the largest gains.

SARS-CoV-2 mutational cascades and the risk of hyper-exponential growth.

The emergence of novel SARS-CoV-2 variants of concern (VOC), in late 2020, with selective transmission advantage and partial immunity escape potential, has been driving further evolution in the pandemic. The timing of mutational evolution and its limits are thus of paramount importance in preparedness planning. Here, we present a model predicting the pattern of epidemic growth including the emergence of variants through mutation. It is based on the SEIR (Susceptible, Exposed, Infected, Removed) model, but its equations are modified according to the transmission parameters of novel variants. Since more transmissible strains will drive a further increase in the number of cases, they will also lead to further novel mutations. As one cannot predict whether there is a viral mutational evolutionary limit, we model a cascade that could lead to hyper-exponential growth (HEG) involving the emergence of even more transmissible mutants that could overwhelm any systematic response. Our results are consistent with the timing, since the beginning of the pandemic, of the concurrent and independent emergence of the VOCs. The current dominance of the Delta variant and the need for additional public health measures indicates some of the risks of a possible HEG. We examine conditions that favor the expected appearance of similar variants, thus enabling better preparedness and more targeted research.

An Orchid in Retrograde: Climate-Driven Range Shift Patterns of Ophrys helenae in Greece.

Climate change is regarded as one of the most important threats to plants. Already species around the globe are showing considerable latitudinal and altitudinal shifts. Helen's bee orchid (Ophrys helenae), a Balkan endemic with a distribution center in northwestern Greece, is reported to be expanding east and southwards. Since this southeastern movement goes against the usual expectations, we investigated via Species Distribution Modelling, whether this pattern is consistent with projections based on the species' response to climate change. We predicted the species' future distribution based on three different climate models in two climate scenarios. We also explored the species' potential distribution during the Last Interglacial and the Last Glacial Maximum. O. helenae is projected to shift mainly southeast and experience considerable area changes. The species is expected to become extinct in the core of its current distribution, but to establish a strong presence in the mid- and high-altitude areas of the Central Peloponnese, a region that could have provided shelter in previous climatic extremes.

Butterfly phenology in Mediterranean mountains using space-for-time substitution.

Inferring species' responses to climate change in the absence of long-term time series data is a challenge, but can be achieved by substituting space for time. For example, thermal elevational gradients represent suitable proxies to study phenological responses to warming. We used butterfly data from two Mediterranean mountain areas to test whether mean dates of appearance of communities and individual species show a delay with increasing altitude, and an accompanying shortening in the duration of flight periods. We found a 14-day delay in the mean date of appearance per kilometer increase in altitude for butterfly communities overall, and an average 23-day shift for 26 selected species, alongside average summer temperature lapse rates of 3°C per km. At higher elevations, there was a shortening of the flight period for the community of 3 days/km, with an 8.8-day average decline per km for individual species. Rates of phenological delay differed significantly between the two mountain ranges, although this did not seem to result from the respective temperature lapse rates. These results suggest that climate warming could lead to advanced and lengthened flight periods for Mediterranean mountain butterfly communities. However, although multivoltine species showed the expected response of delayed and shortened flight periods at higher elevations, univoltine species showed more pronounced delays in terms of species appearance. Hence, while projections of overall community responses to climate change may benefit from space-for-time substitutions, understanding species-specific responses to local features of habitat and climate may be needed to accurately predict the effects of climate change on phenology.

Implications of salep collection for the conservation of the Elder-flowered orchid (Dactylorhiza sambucina) in Epirus, Greece.

BACKGROUND: In Epirus, Greece, orchids have been traditionally harvested for the production of salep, a beverage made from their tubers. Over-collection of orchids for salep is believed to be a growing threat to wild species, yet very little research has concentrated on orchid populations in the wild. Here, we studied the impact of salep collection on population demographic parameters and uniformity of distribution patterns of the Elder-flowered orchid, Dactylorhiza sambucina, the most commonly collected orchid in northern Greece. METHODS: We carried out fieldwork in four meadows where salep harvesting occurs, and conducted interviews in villages close to these sites. Fieldwork focused on the demographic parameters of orchid populations and on the characteristics of their habitat (natural-anthropogenic). We also measured population size and distribution, extent and multi-scale density, comparing distributions to Poisson and fractal models. RESULTS: According to interviews, salep collection by the local community has decreased, contrary to collection by people outside the community, which is increasing. Interviewees did not believe that orchid abundance was higher in the past; they claim that it can be very variable. None of the participants seemed aware of the legislation to conserve orchids. Demographic parameters did not seem to be strongly dependent on whether it was a harvested and non-harvested sites and population density was greatest in the site of highest collection pressure. CONCLUSIONS: Our findings show that salep collection is still ongoing in Epirus. Our interview results and our population study indicate that current levels of collection are not significantly affecting the abundance of the Elder-flowered orchid in Epirus subalpine meadows. However, the expanding commercial collection could reach levels that threaten the species. There is a need for a longer-term monitoring of these orchid populations, and a more effective modeling of the species' response to different harvesting pressures.

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.

Targeted habitat restoration can reduce extinction rates in fragmented forests.

The Eastern Arc Mountains of Tanzania and the Atlantic Forest of Brazil are two of the most fragmented biodiversity hotspots. Species-area relationships predict that their habitat fragments will experience a substantial loss of species. Most of these extinctions will occur over an extended time, and therefore, reconnecting fragments could prevent species losses and allow locally extinct species to recolonize former habitats. An empirical relaxation half-life vs. area relationship for tropical bird communities estimates the time that it takes to lose one-half of all species that will be eventually lost. We use it to estimate the increase in species persistence by regenerating a forest connection 1 km in width among the largest and closest fragments at 11 locations. In the Eastern Arc Mountains, regenerating 8,134 ha of forest would create >316,000 ha in total of restored contiguous forest. More importantly, it would increase the persistence time for species by a factor of 6.8 per location or ∼2,272 years, on average, relative to individual fragments. In the Atlantic Forest, regenerating 6,452 ha of forest would create >251,000 ha in total of restored contiguous forest and enhance species persistence by a factor of 13.0 per location or ∼5,102 years, on average, relative to individual fragments. Rapidly regenerating forest among fragments is important, because mean time to the first determined extinction across all fragments is 7 years. We estimate the cost of forest regeneration at $21-$49 million dollars. It could provide one of the highest returns on investment for biodiversity conservation worldwide.

Campanula lingulata populations on Mt. Olympus, Greece: where's the "abundant centre"?

BACKGROUND: The abundant-centre hypothesis (ACH) assumes that a species becomes more abundant at the centre of its range, where the environmental conditions are most favorable. As we move away from this centre, abundance and occupancy decline. Although this is obvious intuitively, efforts to confirm the hypothesis have often failed. We investigated the abundance patterns of Campanula lingulata across its altitudinal range on Mt. Olympus, Greece, in order to evaluate the "abundant centre" hypothesis along an elevation gradient. Furthermore, we explored the species' presence and dynamics at multiple spatial scales. METHODS: We recorded flowering individuals during the summer months of 2012 and 2013 along a series of transects defined by paths. We investigated whether the probability of acquiring a larger number of individuals is larger toward the centre of its altitudinal distribution. We also calculated mean presence and turnover at different spatial scales that ranged from quadrats of 10 × 10 m2 to about 10 × 10 km2. RESULTS: We were able to identify an abundant centre but only for one of the years of sampling. During the second year, we noted a two-peak abundance pattern; with the first peak occurring at 650-750 m and the second at 1100-1300 m. Variability in the species-presence pattern is observed across a wide range of spatial scales. The pattern along the transect displays fractal characteristics, consistent with a dimension of 0.24-0.29. We found substantial changes of state between the 2 years at all resolutions. CONCLUSIONS: Our results do not contradict the ACH, but indicate that ecological distributions exhibit types of variability that make the detection of abundant centres more difficult than expected. When a random fractal disturbance is superimposed upon an abundant centre, we can expect a pattern in which the centre is difficult to discern from a single instance. A multi-resolution or fractal approach to environmental variability is a promising approach for describing this phenomenon.

A forecast for extinction debt in the presence of speciation.

Predicting biodiversity relaxation following a disturbance is of great importance to conservation biology. Recently-developed models of stochastic community assembly allow us to predict the evolution of communities on the basis of mechanistic processes at the level of individuals. The neutral model of biodiversity, in particular, has provided closed-form solutions for the relaxation of biodiversity in isolated communities (no immigration or speciation). Here, we extend these results by deriving a relaxation curve for a neutral community in which new species are introduced through the mechanism of random fission speciation (RFS). The solution provides simple closed-form expressions for the equilibrium species richness, the relaxation time and the species-individual curve, which are good approximation to the more complicated formulas existing for the same model. The derivation of the relaxation curve is based on the assumption of a broken-stick species-abundance distribution (SAD) as an initial community configuration; yet for commonly observed SADs, the maximum deviation from the curve does not exceed 10%. Importantly, the solution confirms theoretical results and observations showing that the relaxation time increases with community size and thus habitat area. Such simple and analytically tractable models can help crystallize our ideas on the leading factors affecting biodiversity loss.

Dynamics of extinction debt across five taxonomic groups.

Species extinction following habitat loss is well documented. However, these extinctions do not happen immediately. The biodiversity surplus (extinction debt) declines with some delay through the process of relaxation. Estimating the time constants of relaxation, mainly the expected time to first extinction and the commonly used time for half the extinction debt to be paid off (half-life), is crucial for conservation purposes. Currently, there is no agreement on the rate of relaxation and the factors that it depends on. Here we find that half-life increases with area for all groups examined in a large meta-analysis of extinction data. A common pattern emerges if we use average number of individuals per species before habitat loss as an area index: for mammals, birds, reptiles and plants, the relationship has an exponent close to a half. We also find that the time to first determined extinction is short and increases slowly with area.

Extinction risk of soil biota.

No species lives on earth forever. Knowing when and why species go extinct is crucial for a complete understanding of the consequences of anthropogenic activity, and its impact on ecosystem functioning. Even though soil biota play a key role in maintaining the functioning of ecosystems, the vast majority of existing studies focus on aboveground organisms. Many questions about the fate of belowground organisms remain open, so the combined effort of theorists and applied ecologists is needed in the ongoing development of soil extinction ecology.

Terrestrial basking sea turtles are responding to spatio-temporal sea surface temperature patterns.

Naturalists as early as Darwin observed terrestrial basking in green turtles (Chelonia mydas), but the distribution and environmental influences of this behaviour are poorly understood. Here, we examined 6 years of daily basking surveys in Hawaii and compared them with the phenology of local sea surface temperatures (SST). Data and models indicated basking peaks when SST is coolest, and we found this timeline consistent with bone stress markings. Next, we assessed the decadal SST profiles for the 11 global green turtle populations. Basking generally occurs when winter SST falls below 23°C. From 1990 to 2014, the SST for these populations warmed an average 0.04°C yr(-1) (range 0.01-0.09°C yr(-1)); roughly three times the observed global average over this period. Owing to projected future warming at basking sites, we estimated terrestrial basking in green turtles may cease globally by 2100. To predict and manage for future climate change, we encourage a more detailed understanding for how climate influences organismal biology.

Fungi in a changing world: growth rates will be elevated, but spore production may decrease in future climates.

Very little is known about the impact of climate change on fungi and especially on spore production. Fungal spores can be allergenic, thus being important for human health. The aim of this study was to investigate how climate change influences the responsive ability of fungi by simulating differing environmental regimes. Fungal species with high spore allergenic potential and atmospheric abundance were grown and experimentally examined under a variety of temperatures and different nutrient availability. Each represented the average decadal air temperature of the 1980s, 1990s and 2000s in the UK, along with an Intergovernmental Panel on Climate Change (IPCC) climate change scenario for 2100. All tests were run on six fungal species: Alternaria alternata, Aspergillus niger, Botrytis cinerea, Cladosporium cladosporioides, Cladosporium oxysporum and Epicoccum purpurascens. Mycelium growth rate and spore production were examined on each single species and competitive capacity among species combinations in pairs. All fungal species grew faster at higher temperatures, and this was more pronounced for the temperature projection in 2100. Most species grew faster when there was lower nutrient availability. Exceptions were the species with the highest growth rate (E. purpurascens) and with the highest competition capacity (A. alternata). Most species (except for E. purpurascens) produced more spores in the richer nutrient medium but fewer as temperature increased. C. cladosporioides was an exception, exponentially increasing its spore production in the temperature of the 2100 scenario. Regarding competitive capacity, no species displayed any significant alterations within the environmental range checked. It is suggested that in future climates, fungi will display dramatic growth responses, with faster mycelium growth and lower spore production, with questions risen on relevant allergen potential.

Signals of climate change in butterfly communities in a Mediterranean protected area.

The European protected-area network will cease to be efficient for biodiversity conservation, particularly in the Mediterranean region, if species are driven out of protected areas by climate warming. Yet, no empirical evidence of how climate change influences ecological communities in Mediterranean nature reserves really exists. Here, we examine long-term (1998-2011/2012) and short-term (2011-2012) changes in the butterfly fauna of Dadia National Park (Greece) by revisiting 21 and 18 transects in 2011 and 2012 respectively, that were initially surveyed in 1998. We evaluate the temperature trend for the study area for a 22-year-period (1990-2012) in which all three butterfly surveys are included. We also assess changes in community composition and species richness in butterfly communities using information on (a) species' elevational distributions in Greece and (b) Community Temperature Index (calculated from the average temperature of species' geographical ranges in Europe, weighted by species' abundance per transect and year). Despite the protected status of Dadia NP and the subsequent stability of land use regimes, we found a marked change in butterfly community composition over a 13 year period, concomitant with an increase of annual average temperature of 0.95°C. Our analysis gave no evidence of significant year-to-year (2011-2012) variability in butterfly community composition, suggesting that the community composition change we recorded is likely the consequence of long-term environmental change, such as climate warming. We observe an increased abundance of low-elevation species whereas species mainly occurring at higher elevations in the region declined. The Community Temperature Index was found to increase in all habitats except agricultural areas. If equivalent changes occur in other protected areas and taxonomic groups across Mediterranean Europe, new conservation options and approaches for increasing species' resilience may have to be devised.

Species-area relationships and extinction forecasts.

The species-area relationship (SAR) predicts that smaller areas contain fewer species. This is the basis of the SAR method that has been used to forecast large numbers of species committed to extinction every year due to deforestation. The method has a number of issues that must be handled with care to avoid error. These include the functional form of the SAR, the choice of equation parameters, the sampling procedure used, extinction debt, and forest regeneration. Concerns about the accuracy of the SAR technique often cite errors not much larger than the natural scatter of the SAR itself. Such errors do not undermine the credibility of forecasts predicting large numbers of extinctions, although they may be a serious obstacle in other SAR applications. Very large errors can arise from misinterpretation of extinction debt, inappropriate functional form, and ignoring forest regeneration. Major challenges remain to understand better the relationship between sampling protocol and the functional form of SARs and the dynamics of relaxation, especially in continental areas, and to widen the testing of extinction forecasts.