The phylogeography of Middle Eastern tree frogs in Israel

Western Palearctic treefrogs of the genus Hyla provide an example of a morphologically and ecologically cryptic group. Up to three distinct Hyla species have been proposed as resident in Israel and this number has consistently been subject to taxonomical debates. Here, we analyzed 16S rRNA and COI gene fragments of 658 individuals sampled at 47 pools in nine regions across Israel and the West Bank in order to resolve the taxonomic status of Hyla frogs. We generated both Bayesian and Maximum Likelihood phylogenies, and constructed time-calibrated trees to provide an evolutionary and historical context of sequence variations. We further applied SAMOVA as well as Monmonier's maximum-difference algorithm to study the genetic structure among populations and to identify potential zones acting as barriers to gene flow across locations. Our results revealed two distinct haplogroups for each gene fragment, with 95% CI divergence times dated from 8.9-17.1 Mya (16S) and 7.1-23.6 Mya (COI), respectively. SAMOVA and barrier analyses partitioned the populations into three groups. Our results highlight that, while there are probably only two Hyla species in Israel, one population of one of the species might qualify as a separate evolutionarily significant unit. Our findings elucidate the taxonomic status of Hyla frogs in Israel and provide the basis for determining appropriate management and conservation priorities.

Using social media records to inform conservation planning

Citizen science plays a crucial role in helping monitor biodiversity and inform conservation. With the widespread use of smartphones, many people share biodiversity information on social media, but this information is still not widely used in conservation. Focusing on Bangladesh, a tropical megadiverse and mega-populated country, we examined the importance of social media records in conservation decision-making. We collated species distribution records for birds and butterflies from Facebook and Global Biodiversity Information Facility (GBIF), grouped them into GBIF-only and combined GBIF and Facebook data, and investigated the differences in identifying critical conservation areas. Adding Facebook data to GBIF data improved the accuracy of systematic conservation planning assessments by identifying additional important conservation areas in the northwest, southeast, and central parts of Bangladesh, extending priority conservation areas by 4,000-10,000 km2 . Community efforts are needed to drive the implementation of the ambitious Kunming-Montreal Global Biodiversity Framework targets, especially in megadiverse tropical countries with a lack of reliable and up-to-date species distribution data. We highlight that conservation planning can be enhanced by including available data gathered from social media platforms.

Evaluating global interest in biodiversity and conservation

The first target of the Convention for Biological Diversity (Aichi target 1) was to increase public awareness of the values of biodiversity and actions needed to conserve it-a key prerequisite for other conservation targets. Monitoring success in achieving this target at a global scale has been difficult; however, increased digitization of human life in recent decades has made it easier to measure people's interests at an unprecedented scale and allows for a more comprehensive evaluation of Aichi target 1 than previously attempted. We used Google search volume data for over a thousand search terms related to different aspects of biodiversity and conservation to evaluate global interest in biodiversity and its conservation. We also investigated the correlation of interest in biodiversity and conservation across countries to variables related to biodiversity, economy, demography, research, education, internet use, and presence of environmental organizations. From 2013 to 2020, global searches for biodiversity components increased, driven mostly by searches for charismatic fauna (59% of searches were for mammal species). Searches for conservation actions, driven mostly by searches for national parks, decreased since 2019, likely due to the COVID-19 pandemic. Economic inequality was negatively correlated with interest in biodiversity and conservation, whereas purchasing power was indirectly positively correlated with higher levels of education and research. Our results suggest partial success toward achieving Aichi target 1 in that interest in biodiversity increased widely, but not for conservation. We suggest that increased outreach and education efforts aimed at neglected aspects of biodiversity and conservation are still needed. Popular topics in biodiversity and conservation could be leveraged to increase awareness of other topics with attention to local socioeconomic contexts.

Chemical signaling glands are unlinked to species diversification in lizards

Sexual selection has long been thought to increase species diversification. Sexually selected traits, such as sexual signals that contribute to reproductive isolation, were thought to promote diversification. However, studies exploring links between sexually selected traits and species diversification have thus far primarily focused on visual or acoustic signals. Many animals often employ chemical signals (i.e., pheromones) for sexual communications, but large-scale analyses on the role of chemical communications in driving species diversification have been missing. Here, for the first time, we investigate whether traits associated with chemical communications-the presence of follicular epidermal glands-promote diversification across 6,672 lizard species. In most analyses, we found no strong association between the presence of follicular epidermal glands and species diversification rates, either across all lizard species or at lower phylogenetic scales. Previous studies suggest that follicular gland secretions act as species recognition signals that prevent hybridization during speciation in lizards. However, we show that geographic range overlap was no different in sibling species pairs with and without follicular epidermal glands. Together, these results imply that either follicular epidermal glands do not primarily function in sexual communications or sexually selected traits in general (here chemical communication) have a limited effect on species diversification. In our additional analysis accounting for sex-specific differences in glands, we again found no detectable effect of follicular epidermal glands on species diversification rates. Thus, our study challenges the general role of sexually selected traits in broad-scale species diversification patterns.

Global Protected Areas as refuges for amphibians and reptiles under climate change

Protected Areas (PAs) are the cornerstone of biodiversity conservation. Here, we collated distributional data for >14,000 (~70% of) species of amphibians and reptiles (herpetofauna) to perform a global assessment of the conservation effectiveness of PAs using species distribution models. Our analyses reveal that >91% of herpetofauna species are currently distributed in PAs, and that this proportion will remain unaltered under future climate change. Indeed, loss of species' distributional ranges will be lower inside PAs than outside them. Therefore, the proportion of effectively protected species is predicted to increase. However, over 7.8% of species currently occur outside PAs, and large spatial conservation gaps remain, mainly across tropical and subtropical moist broadleaf forests, and across non-high-income countries. We also predict that more than 300 amphibian and 500 reptile species may go extinct under climate change over the course of the ongoing century. Our study highlights the importance of PAs in providing herpetofauna with refuge from climate change, and suggests ways to optimize PAs to better conserve biodiversity worldwide.

Future temperature extremes threaten land vertebrates

The frequency, duration, and intensity of extreme thermal events are increasing and are projected to further increase by the end of the century^1,2. Despite the considerable consequences of temperature extremes on biological systems^3-8, we do not know which species and locations are most exposed worldwide. Here we provide a global assessment of land vertebrates' exposures to future extreme thermal events. We use daily maximum temperature data from 1950 to 2099 to quantify future exposure to high frequency, duration, and intensity of extreme thermal events to land vertebrates. Under a high greenhouse gas emission scenario (Shared Socioeconomic Pathway 5-8.5 (SSP5-8.5); 4.4 °C warmer world), 41.0% of all land vertebrates (31.1% mammals, 25.8% birds, 55.5% amphibians and 51.0% reptiles) will be exposed to extreme thermal events beyond their historical levels in at least half their distribution by 2099. Under intermediate-high (SSP3-7.0; 3.6 °C warmer world) and intermediate (SSP2-4.5; 2.7 °C warmer world) emission scenarios, estimates for all vertebrates are 28.8% and 15.1%, respectively. Importantly, a low-emission future (SSP1-2.6, 1.8 °C warmer world) will greatly reduce the overall exposure of vertebrates (6.1% of species) and can fully prevent exposure in many species assemblages. Mid-latitude assemblages (desert, shrubland, and grassland biomes), rather than tropics^9,10, will face the most severe exposure to future extreme thermal events. By 2099, under SSP5-8.5, on average 3,773 species of land vertebrates (11.2%) will face extreme thermal events for more than half a year period. Overall, future extreme thermal events will force many species and assemblages into constant severe thermal stress. Deep greenhouse gas emissions cuts are urgently needed to limit species' exposure to thermal extremes.

Automated assessment reveals that the extinction risk of reptiles is widely underestimated across space and phylogeny

The Red List of Threatened Species, published by the International Union for Conservation of Nature (IUCN), is a crucial tool for conservation decision-making. However, despite substantial effort, numerous species remain unassessed or have insufficient data available to be assigned a Red List extinction risk category. Moreover, the Red Listing process is subject to various sources of uncertainty and bias. The development of robust automated assessment methods could serve as an efficient and highly useful tool to accelerate the assessment process and offer provisional assessments. Here, we aimed to (1) present a machine learning–based automated extinction risk assessment method that can be used on less known species; (2) offer provisional assessments for all reptiles—the only major tetrapod group without a comprehensive Red List assessment; and (3) evaluate potential effects of human decision biases on the outcome of assessments. We use the method presented here to assess 4,369 reptile species that are currently unassessed or classified as Data Deficient by the IUCN. The models used in our predictions were 90% accurate in classifying species as threatened/nonthreatened, and 84% accurate in predicting specific extinction risk categories. Unassessed and Data Deficient reptiles were considerably more likely to be threatened than assessed species, adding to mounting evidence that these species warrant more conservation attention. The overall proportion of threatened species greatly increased when we included our provisional assessments. Assessor identities strongly affected prediction outcomes, suggesting that assessor effects need to be carefully considered in extinction risk assessments. Regions and taxa we identified as likely to be more threatened should be given increased attention in new assessments and conservation planning. Lastly, the method we present here can be easily implemented to help bridge the assessment gap for other less known taxa.

A global reptile assessment highlights shared conservation needs of tetrapods

Comprehensive assessments of species’ extinction risks have documented the extinction crisis¹ and underpinned strategies for reducing those risks². Global assessments reveal that, among tetrapods, 40.7% of amphibians, 25.4% of mammals and 13.6% of birds are threatened with extinction³. Because global assessments have been lacking, reptiles have been omitted from conservation-prioritization analyses that encompass other tetrapods^4–7. Reptiles are unusually diverse in arid regions, suggesting that they may have different conservation needs⁶. Here we provide a comprehensive extinction-risk assessment of reptiles and show that at least 1,829 out of 10,196 species (21.1%) are threatened—confirming a previous extrapolation⁸ and representing 15.6 billion years of phylogenetic diversity. Reptiles are threatened by the same major factors that threaten other tetrapods—agriculture, logging, urban development and invasive species—although the threat posed by climate change remains uncertain. Reptiles inhabiting forests, where these threats are strongest, are more threatened than those in arid habitats, contrary to our prediction. Birds, mammals and amphibians are unexpectedly good surrogates for the conservation of reptiles, although threatened reptiles with the smallest ranges tend to be isolated from other threatened tetrapods. Although some reptiles—including most species of crocodiles and turtles—require urgent, targeted action to prevent extinctions, efforts to protect other tetrapods, such as habitat preservation and control of trade and invasive species, will probably also benefit many reptiles.

An extinction-risk assessment of reptiles shows that at least 21.1% of species are threatened by factors such as agriculture, logging, urban development and invasive species, and that efforts to protect birds, mammals and amphibians probably also benefit many reptiles.

Societal extinction of species

The ongoing global biodiversity crisis not only involves biological extinctions, but also the loss of experience and the gradual fading of cultural knowledge and collective memory of species. We refer to this phenomenon as 'societal extinction of species' and apply it to both extinct and extant taxa. We describe the underlying concepts as well as the mechanisms and factors that affect this process, discuss its main implications, and identify mitigation measures. Societal extinction is cognitively intractable, but it is tied to biological extinction and thus has important consequences for conservation policy and management. It affects societal perceptions of the severity of anthropogenic impacts and of true extinction rates, erodes societal support for conservation efforts, and causes the loss of cultural heritage.

Global COVID-19 lockdown highlights humans as both threats and custodians of the environment

The global lockdown to mitigate COVID-19 pandemic health risks has altered human interactions with nature. Here, we report immediate impacts of changes in human activities on wildlife and environmental threats during the early lockdown months of 2020, based on 877 qualitative reports and 332 quantitative assessments from 89 different studies. Hundreds of reports of unusual species observations from around the world suggest that animals quickly responded to the reductions in human presence. However, negative effects of lockdown on conservation also emerged, as confinement resulted in some park officials being unable to perform conservation, restoration and enforcement tasks, resulting in local increases in illegal activities such as hunting. Overall, there is a complex mixture of positive and negative effects of the pandemic lockdown on nature, all of which have the potential to lead to cascading responses which in turn impact wildlife and nature conservation. While the net effect of the lockdown will need to be assessed over years as data becomes available and persistent effects emerge, immediate responses were detected across the world. Thus, initial qualitative and quantitative data arising from this serendipitous global quasi-experimental perturbation highlights the dual role that humans play in threatening and protecting species and ecosystems. Pathways to favorably tilt this delicate balance include reducing impacts and increasing conservation effectiveness.

Areas of global importance for conserving terrestrial biodiversity, carbon and water

To meet the ambitious objectives of biodiversity and climate conventions, the international community requires clarity on how these objectives can be operationalized spatially and how multiple targets can be pursued concurrently. To support goal setting and the implementation of international strategies and action plans, spatial guidance is needed to identify which land areas have the potential to generate the greatest synergies between conserving biodiversity and nature's contributions to people. Here we present results from a joint optimization that minimizes the number of threatened species, maximizes carbon retention and water quality regulation, and ranks terrestrial conservation priorities globally. We found that selecting the top-ranked 30% and 50% of terrestrial land area would conserve respectively 60.7% and 85.3% of the estimated total carbon stock and 66% and 89.8% of all clean water, in addition to meeting conservation targets for 57.9% and 79% of all species considered. Our data and prioritization further suggest that adequately conserving all species considered (vertebrates and plants) would require giving conservation attention to ~70% of the terrestrial land surface. If priority was given to biodiversity only, managing 30% of optimally located land area for conservation may be sufficient to meet conservation targets for 81.3% of the terrestrial plant and vertebrate species considered. Our results provide a global assessment of where land could be optimally managed for conservation. We discuss how such a spatial prioritization framework can support the implementation of the biodiversity and climate conventions.

Global determinants and conservation of evolutionary and geographic rarity in land vertebrates

Deciphering global trends in phylogenetic endemism is crucial for understanding broad-scale evolutionary patterns and the conservation of key elements of biodiversity. However, knowledge to date on global phylogenetic endemism and its determinants has been lacking. Here, we conduct the first global analysis of phylogenetic endemism patterns of land vertebrates (>30,000 species), their environmental correlates, and threats. We found that low temperature seasonality and high topographic heterogeneity were the main global determinants of phylogenetic endemism. While phylogenetic endemism hotspots cover 22% of Earth, these regions currently have a high human footprint, low natural land cover, minimal protection, and will be greatly affected by climate change. Evolutionarily unique, narrow-range species are crucial for sustaining biodiversity in the face of environmental change. Our global study advances the current understanding of this imperilled yet previously overlooked facet of biodiversity.

Reduced human activity in shallow reefs during the COVID-19 pandemic increases fish evenness

The COVID-19 pandemic provides a rare opportunity to examine effects of people on natural systems and processes. Here, we collected fish diversity data from coral reefs at the Israeli Gulf of Aqaba during and after the COVID-19 lockdown. We examined beach entrances to the reef, nearby shallow reefs and deeper areas exposed mostly to divers. We found that the lockdown elicited a behavioral response that resulted in elevated species richness at designated reef entrances, predominantly influenced by increased evenness without changes to total abundances. This effect was observed both at the local scale and when several beach entrances were aggregated together. Consequently, non-extractive human activities may have substantial short-term impacts on fish diversity. Our insights could help designate guidelines to manage visitor impacts on coral reefs and aid in their prolonged persistence.

Digital data sources and methods for conservation culturomics

Ongoing loss of biological diversity is primarily the result of unsustainable human behavior. Thus, the long-term success of biodiversity conservation depends on a thorough understanding of human-nature interactions. Such interactions are ubiquitous but vary greatly in time and space and are difficult to monitor efficiently at large spatial scales. However, the Information Age also provides new opportunities to better understand human-nature interactions because many aspects of daily life are recorded in a variety of digital formats. The emerging field of conservation culturomics aims to take advantage of digital data sources and methods to study human-nature interactions and thus to provide new tools for studying conservation at relevant temporal and spatial scales. Nevertheless, technical challenges associated with the identification, access, and analysis of relevant data hamper the wider adoption of culturomics methods. To help overcome these barriers, we propose a conservation culturomics research framework that addresses data acquisition, analysis, and inherent biases. The main sources of culturomic data include web pages, social media, and other digital platforms from which metrics of content and engagement can be obtained. Obtaining raw data from these platforms is usually desirable but requires careful consideration of how to access, store, and prepare the data for analysis. Methods for data analysis include network approaches to explore connections between topics, time-series analysis for temporal data, and spatial modeling to highlight spatial patterns. Outstanding challenges associated with culturomics research include issues of interdisciplinarity, ethics, data biases, and validation. The practical guidance we offer will help conservation researchers and practitioners identify and obtain the necessary data and carry out appropriate analyses for their specific questions, thus facilitating the wider adoption of culturomics approaches for conservation applications.

Combining culturomic sources to uncover trends in popularity and seasonal interest in plants

Culturomic tools enable the exploration of trends in human-nature interactions, although they entail inherent biases and necessitate careful validation. Furthermore, people may engage with nature across different culturomic data sets differently. We evaluated people's digital interest and engagement with plant species based on Wikipedia and Google data and explored the conservation implications of these temporal interest patterns. As a case study, we explored the digital footprints of the most popular plant species in Israel. We analyzed 4 years of daily page views from Hebrew Wikipedia and 10 years of daily Google search volume in Israel. We modeled popularity of plant species in these 2 data sets based on a suite of plant attributes. We further explored the seasonal trends of people's interest in each species. We found differences in how people interacted digitally with plants in Wikipedia and Google. Overall, in Google, searches for species that have utility to humans were more common, whereas in Wikipedia, plants that serve as cultural emblems received more attention. Furthermore, in Google, popular species attracted more attention over time, opposite to the trend in Wikipedia. In Google, interest in species with short bloom duration exhibited more pronounced seasonal patterns, whereas in Wikipedia, seasonality of interest increased as bloom duration increased. Together, our results suggest that people's digital interactions with nature may be inherently different depending on the sources explored, which may affect use of this information for conservation. Although culturomics holds much promise, better understanding of its underpinnings is important when translating insights into conservation actions.

Using Wikipedia to measure public interest in biodiversity and conservation

The recent growth of online big data offers opportunities for rapid and inexpensive measurement of public interest. Conservation culturomics is an emerging research area that uses online data to study human-nature relationships for conservation. Methods for conservation culturomics, though promising, are still being developed and refined. We considered the potential of Wikipedia, the online encyclopedia, as a resource for conservation culturomics and outlined methods for using Wikipedia data in conservation. Wikipedia's large size, widespread use, underlying data structure, and open access to both its content and usage analytics make it well suited to conservation culturomics research. Limitations of Wikipedia data include the lack of location information associated with some metadata and limited information on the motivations of many users. Seven methodological steps to consider when using Wikipedia data in conservation include metadata selection, temporality, taxonomy, language representation, Wikipedia geography, physical and biological geography, and comparative metrics. Each of these methodological decisions can affect measures of online interest. As a case study, we explored these themes by analyzing 757 million Wikipedia page views associated with the Wikipedia pages for 10,099 species of birds across 251 Wikipedia language editions. We found that Wikipedia data have the potential to generate insight for conservation and are particularly useful for quantifying patterns of public interest at large scales.

Different solutions lead to similar life history traits across the great divides of the amniote tree of life

Amniote vertebrates share a suite of extra-embryonic membranes that distinguish them from anamniotes. Other than that, however, their reproductive characteristics could not be more different. They differ in basic ectothermic vs endothermic physiology, in that two clades evolved powered flight, and one clade evolved a protective shell. In terms of reproductive strategies, some produce eggs and others give birth to live young, at various degrees of development. Crucially, endotherms provide lengthy parental care, including thermal and food provisioning—whereas ectotherms seldom do. These differences could be expected to manifest themselves in major differences between clades in quantitative reproductive traits. We review the reproductive characteristics, and the distributions of brood sizes, breeding frequencies, offspring sizes and their derivatives (yearly fecundity and biomass production rates) of the four major amniote clades (mammals, birds, turtles and squamates), and several major subclades (birds: Palaeognathae, Galloanserae, Neoaves; mammals: Metatheria and Eutheria). While there are differences between these clades in some of these traits, they generally show similar ranges, distribution shapes and central tendencies across birds, placental mammals and squamates. Marsupials and turtles, however, differ in having smaller offspring, a strategy which subsequently influences other traits.

iNaturalist insights illuminate COVID-19 effects on large mammals in urban centers

Restricted human activity during the COVID-19 pandemic raised global attention to the presence of wildlife in cities. Here, we analyzed iNaturalist observations of prominent wildlife species around North-American urban centers, before and during the COVID-19 pandemic outbreak. We suggest that the popular notion of 'wildlife reclaiming cities' may have been exaggerated. We found that while pumas ventured deeper into urban habitats during the COVID-19 pandemic, bears, bobcats, coyotes, and moose did not. Species differential behavioral responses may highlight their evolutionary history cohabiting human habitats. Nevertheless, our results highlight the importance of urban nature for people during the pandemic. Our insights could help manage urban wildlife, better plan greenspaces, and promote positive nature engagements.

Global priorities for conservation of reptilian phylogenetic diversity in the face of human impacts

Phylogenetic diversity measures are increasingly used in conservation planning to represent aspects of biodiversity beyond that captured by species richness. Here we develop two new metrics that combine phylogenetic diversity and the extent of human pressure across the spatial distribution of species - one metric valuing regions and another prioritising species. We evaluate these metrics for reptiles, which have been largely neglected in previous studies, and contrast these results with equivalent calculations for all terrestrial vertebrate groups. We find that regions under high human pressure coincide with the most irreplaceable areas of reptilian diversity, and more than expected by chance. The highest priority reptile species score far above the top mammal and bird species, and reptiles include a disproportionate number of species with insufficient extinction risk data. Data Deficient species are, in terms of our species-level metric, comparable to Critically Endangered species and therefore may require urgent conservation attention.

Using machine learning to disentangle homonyms in large text corpora

Systematic reviews are an increasingly popular decision-making tool that provides an unbiased summary of evidence to support conservation action. These reviews bridge the gap between researchers and managers by presenting a comprehensive overview of all studies relating to a particular topic and identify specifically where and under which conditions an effect is present. However, several technical challenges can severely hinder the feasibility and applicability of systematic reviews, for example, homonyms (terms that share spelling but differ in meaning). Homonyms add noise to search results and cannot be easily identified or removed. We developed a semiautomated approach that can aid in the classification of homonyms among narratives. We used a combination of automated content analysis and artificial neural networks to quickly and accurately sift through large corpora of academic texts and classify them to distinct topics. As an example, we explored the use of the word reintroduction in academic texts. Reintroduction is used within the conservation context to indicate the release of organisms to their former native habitat; however, a Web of Science search for this word returned thousands of publications in which the term has other meanings and contexts. Using our method, we automatically classified a sample of 3000 of these publications with over 99% accuracy, relative to a manual classification. Our approach can be used easily with other homonyms and can greatly facilitate systematic reviews or similar work in which homonyms hinder the harnessing of large text corpora. Beyond homonyms we see great promise in combining automated content analysis and machine-learning methods to handle and screen big data for relevant information in conservation science.

The contextual separation of lateral white line patterns in chameleons

While many animals display different colour patterns that signal different messages, some species use various tactics to separate between colour and pattern displays. The common chameleon (Chamaeleo chamaeleon) is capable of rapidly changing and separating among displays of colour patterns and ornaments. We used chameleons to study the contextual role of separation among colour and pattern displays. Specifically, we studied the predominant white badge, which is composed of multiple parts, during different seasons and in different social contexts. We hypothesized that the badge contains important information about the sender and, therefore, would be present during important social contexts. We carried out a series of trials to document the presence/absence of the badge and found that the badge is individually specific and reflects body size. We also revealed that the badge remained fixed throughout other body colour changes, but was replaced by other colour patterns during mating behaviour. During social encounters, additional dark patches delineating the badge appeared, presumably amplifying its signal. Thus, we suggest that the badge constitutes an important feature in intraspecific communication, and is possibly employed to display quality. However, the replacement of the badge by other displays during courtship suggests that during important social events like mating, chameleons transmit exclusive information that is not broadcast by the badge. Our findings demonstrate the importance of separation between colour patterns, and the alternative use of intraspecific colour patterns for specific social contexts in chameleons.

Living quarters of a living fossil-Uncovering the current distribution pattern of the rediscovered Hula painted frog (Latonia nigriventer) using environmental DNA

One of the greatest challenges of effective conservation measures is the correct identification of sites where rare and elusive organisms reside. The recently rediscovered Hula painted frog (Latonia nigriventer) has not been seen for many decades and was therefore categorized extinct. Since its rediscovery in 2011, individuals from the critically endangered species have been found, with great effort, only in four restricted sites. We applied the environmental DNA (eDNA) approach to search for new populations of the Hula painted frog in suitable aquatic habitats. We further used the eDNA data to classify the landscape factors associated with the species distribution and to predict its suitable habitats. We sampled 52 aquatic sites in the Hula Valley during the spring of 2015 and 2016 and amplified the samples with a species-specific qPCR assay. DNA of the Hula painted frog was detected in 22 of the sites, all of which clustered within three main areas. A boosting classification model showed that soil type, vegetation cover and the current and former habitats are all key predictors of the frog's current distribution. Intriguingly, the habitat suitability models reveal a high affinity of the species to its long-lost habitat of the historical wetlands. Our findings encourage a series of informed searches for new populations of this threatened frog and provide guidance for future conservation management programmes. In the era of global conservation crisis of amphibians, developing the eDNA approach, a reliable detection method for many critically endangered and elusive amphibians, is of particular importance.

Possible linkage between neuronal recruitment and flight distance in migratory birds

New neuronal recruitment in an adult animal’s brain is presumed to contribute to brain plasticity and increase the animal’s ability to contend with new and changing environments. During long-distance migration, birds migrating greater distances are exposed to more diverse spatial information. Thus, we hypothesized that greater migration distance in birds would correlate with the recruitment of new neurons into the brain regions involved with migratory navigation. We tested this hypothesis on two Palearctic migrants - reed warblers (Acrocephalus scirpaceus) and turtle doves (Streptopelia turtur), caught in Israel while returning from Africa in spring and summer. Birds were injected with a neuronal birth marker and later inspected for new neurons in brain regions known to play a role in navigation - the hippocampus and nidopallium caudolateral. We calculated the migration distance of each individual by matching feather isotopic values (δ²H and δ¹³C) to winter base-maps of these isotopes in Africa. Our findings suggest a positive correlation between migration distance and new neuronal recruitment in two brain regions - the hippocampus in reed warblers and nidopallium caudolateral in turtle doves. This multidisciplinary approach provides new insights into the ability of the avian brain to adapt to different migration challenges.

A test for a shift in the boundary of the geographical range of a species

One predicted impact of climate change is a poleward shift in the boundaries of species ranges. Existing methods for identifying such a boundary shift based on changes in the observed pattern of occupancy within a grid of cells are sensitive to changes in the overall rate of sightings and their latitudinal distribution that are unconnected to a boundary shift. A formal test for a boundary shift is described that allows for such changes. The test is applied to detect northward shifts in the northern boundary of the Essex skipper (Thymelicus lineola) butterfly and the European goldfinch (Carduelis carduelis) in Great Britain. A shift is detected in the latter case but not in the former. Results from a simulation study are presented showing that the test performs well.

Rueppel’s Snake-eyed Skink, Ablepharus rueppellii (Gray, 1839) (Reptilia: Squamata: Scincidae): distribution extension and geographic range in Israel

We report a new locality for Rueppel’s Snake-eyed skink (Ablepharus rueppellii) in Southern Israel – near Shivta Junction. This record extends the known distribution of this species in Israel by ~25km. We examined all known localities of this species in Israel and the adjacent Sinai Peninsula (Egypt), and discuss some discrepancies between them and currently published range maps, including the one produced by the IUCN.

Bats of a gender flock together: sexual segregation in a subtropical bat

Competition has long been assumed to be a major driver in regulating ecological communities. Intra-specific competition is considered to be maximal as members of the same species use the same ecological niches in a similar way. Many species of animals exhibit great physiological, behavioral, and morphological differences between sexes (sexual dimorphism). Here we report an extreme geographical segregation between the sexes in the greater mouse-tailed bat (Rhinopoma microphyllum). To gain insight into the driving mechanisms of sexual segregation outside the mating season, we collected and integrated environmental, behavioral, physiological, and spatial information. We found that both sexes choose roosts with similar characteristics and the same food type, but use different habitats for different durations. Males forage around cliffs at higher and cooler elevations while females forage in lowlands around a river delta. We suggest that it is their different physiological and social needs, and not competition, that drives sexual segregation in this species.

Modeling and statistical analysis of the spatio-temporal patterns of seasonal influenza in Israel

Background

Seasonal influenza outbreaks are a serious burden for public health worldwide and cause morbidity to millions of people each year. In the temperate zone influenza is predominantly seasonal, with epidemics occurring every winter, but the severity of the outbreaks vary substantially between years. In this study we used a highly detailed database, which gave us both temporal and spatial information of influenza dynamics in Israel in the years 1998–2009. We use a discrete-time stochastic epidemic SIR model to find estimates and credible confidence intervals of key epidemiological parameters.

Findings

Despite the biological complexity of the disease we found that a simple SIR-type model can be fitted successfully to the seasonal influenza data. This was true at both the national levels and at the scale of single cities.The effective reproductive number R_e varies between the different years both nationally and among Israeli cities. However, we did not find differences in R_e between different Israeli cities within a year. R_e was positively correlated to the strength of the spatial synchronization in Israel. For those years in which the disease was more “infectious”, then outbreaks in different cities tended to occur with smaller time lags. Our spatial analysis demonstrates that both the timing and the strength of the outbreak within a year are highly synchronized between the Israeli cities. We extend the spatial analysis to demonstrate the existence of high synchrony between Israeli and French influenza outbreaks.

Conclusions

The data analysis combined with mathematical modeling provided a better understanding of the spatio-temporal and synchronization dynamics of influenza in Israel and between Israel and France. Altogether, we show that despite major differences in demography and weather conditions intra-annual influenza epidemics are tightly synchronized in both their timing and magnitude, while they may vary greatly between years. The predominance of a similar main strain of influenza, combined with population mixing serve to enhance local and global influenza synchronization within an influenza season.

Modelling the initial phase of an epidemic using incidence and infection network data: 2009 H1N1 pandemic in Israel as a case study

This paper presents new computational and modelling tools for studying the dynamics of an epidemic in its initial stages that use both available incidence time series and data describing the population's infection network structure. The work is motivated by data collected at the beginning of the H1N1 pandemic outbreak in Israel in the summer of 2009. We formulated a new discrete-time stochastic epidemic SIR (susceptible-infected-recovered) model that explicitly takes into account the disease's specific generation-time distribution and the intrinsic demographic stochasticity inherent to the infection process. Moreover, in contrast with many other modelling approaches, the model allows direct analytical derivation of estimates for the effective reproductive number (R(e)) and of their credible intervals, by maximum likelihood and Bayesian methods. The basic model can be extended to include age-class structure, and a maximum likelihood methodology allows us to estimate the model's next-generation matrix by combining two types of data: (i) the incidence series of each age group, and (ii) infection network data that provide partial information of 'who-infected-who'. Unlike other approaches for estimating the next-generation matrix, the method developed here does not require making a priori assumptions about the structure of the next-generation matrix. We show, using a simulation study, that even a relatively small amount of information about the infection network greatly improves the accuracy of estimation of the next-generation matrix. The method is applied in practice to estimate the next-generation matrix from the Israeli H1N1 pandemic data. The tools developed here should be of practical importance for future investigations of epidemics during their initial stages. However, they require the availability of data which represent a random sample of the real epidemic process. We discuss the conditions under which reporting rates may or may not influence our estimated quantities and the effects of bias.

Not so Holy After All

In responses to our paper questioning Israel's great biodiversity, Gavish and Yom-Tov claim that our methods and geographic scope are erroneous, and responsible for our inability to find Israel as diversity hotspot. They maintain that relative to its latitude and realm, Israel is very species-rich. However, our original work corrected for latitude and we highlight the failure of Israel to lie outside the prediction limits of any test in all geographical scopes. We now also analyze richness to test whether realms have parallel slopes in species area curves as Gavish claims and upon which he bases his analysis. We also analyze species richness in the Palearctic realm, calculate prediction limits, and add latitude as a predictor. Moreover, we analyze a new dataset of mammal, bird, and amphibian richness in grid-cells comparing Israeli cell values to the entire world, the Palearctic, and Israel's latitudes. We reject the idea that realms have equal slopes and therefore the Palearctic is not always at a disadvantage compared to other realms. Within the Palearctic realm Israel never lies outside the prediction limits for a country of its area, and adding latitude to this analysis lowered Israel's residual placement. Israel's richness in grid-cells is unexceptional for any taxon at all geographical scopes. In sum, irrespective of the test performed or the geographical region it is compared to, Israel is not a diversity hotspot.

Onset of a pandemic: characterizing the initial phase of the swine flu (H1N1) epidemic in Israel

Background

The swine influenza H1N1 first identified in Mexico, spread rapidly across the globe and is considered the fastest moving pandemic in history. The early phase of an outbreak, in which data is relatively scarce, presents scientific challenges on key issues such as: scale, severity and immunity which are fundamental for establishing sound and rapid policy schemes. Our analysis of an Israeli dataset aims at understanding the spatio-temporal dynamics of H1N1 in its initial phase.

Methods

We constructed and analyzed a unique dataset from Israel on all confirmed cases (between April 26 to July 7, 2009), representing most swine flu cases in this period. We estimated and characterized fundamental epidemiological features of the pandemic in Israel (e.g. effective reproductive number, age-class distribution, at-risk social groups, infections between sexes, and spatial dynamics). Contact data collected during this stage was used to estimate the generation time distribution of the pandemic.

Results

We found a low effective reproductive number (R_e = 1.06), an age-class distribution of infected individuals (skewed towards ages 18-25), at-risk social groups (soldiers and ultra Orthodox Jews), and significant differences in infections between sexes (skewed towards males). In terms of spatial dynamics, the pandemic spread from the central coastal plain of Israel to other regions, with higher infection rates in more densely populated sub-districts with higher income households.

Conclusions

Analysis of high quality data holds much promise in reducing uncertainty regarding fundamental aspects of the initial phase of an outbreak (e.g. the effective reproductive number R_e, age-class distribution, at-risk social groups). The formulation for determining the effective reproductive number R_e used here has many advantages for studying the initial phase of the outbreak since it neither assumes exponential growth of infectives and is independent of the reporting rate. The finding of a low R_e (close to unity threshold), combined with identification of social groups with high transmission rates would have enabled the containment of swine flu during the summer in Israel. Our unique use of contact data provided new insights into the differential dynamics of influenza in different ages and sexes, and should be promoted in future epidemiological studies. Thus our work highlights the importance of conducting a comprehensive study of the initial stage of a pandemic in real time.

The change in genetic diversity down the core-edge gradient in the eastern spadefoot toad (Pelobates syriacus)

Several hypotheses are available to predict change in genetic diversity when approaching peripheral populations. We used the eastern spadefoot toad in Israel as a model system to examine these hypotheses using population genetics analyses and network theory. Our results contradicted most of the predictions from the 'abundant centre' model, that edge populations should have lower density and lower genetic diversity than core populations. Furthermore, dispersal rate between core and peripheral populations is expected to be asymmetric, mostly directed outwards from the core population, but we did not detect such a trend. Our data did not support the hypothesis of no change or a non-linear change in genetic diversity towards the range edge. However, our results did fit the Fisher (The Genetical Theory of Natural Selection, Clarendon Press, Oxford, 1930) hypothesis, which predicts increase in genetic variability from core to edge of distribution. We attributed this finding to the much harsher climatic and abiotic conditions at the edge, which must be tolerated over generations by both tadpoles and post-metamorphic individuals in this region. Finally, our results have significant conservation implications for the survival of this species in Israel, where it is critically endangered. We identified two distinct communities, which are genetically linked through two specific rain pools in the Upper Galilee. Details on the spatial subdivision of this species are cardinal for future management and restoration of temporary wetlands in Israel.

[Mathematical models as tools for studying and developing strategies in the case of a pandemic influenza outbreak]

The current spread of swine flu H1N1 raises serious concerns for public health worldwide. Mathematical modelling has proved to be an essential tool for both developing strategies in preparation for an outbreak and for predicting and evaluating the effectiveness of control policies during an outbreak. Given its growing importance, this article outlines some of the fundamental contributions of mathematical modelling in the study of infectious diseases. The authors review the classical SIR model which has become central to epidemiology, demonstrating basic concepts such as outbreak threshold, the reproductive number Ro and herd immunity. The authors show how the model can be expanded to include different intervention and mitigation strategies, and discuss other biological and social complexities that may be introduced. Finally, the paper illustrates different scenarios for the spread of swine flu in Israel and provides estimates for Reproductive rate (Ro).

Hot-Spot Facts and Artifacts-Questioning Israel's Great Biodiversity

Israel's biological diversity has been praised as being particularly rich in relation to its size; however this assumption was never tested when taking into account the empirical form of the species-area relationship. Here we compared the species richness of different countries to see if the Israeli diversity is exceptionally rich when area is accurately accounted for. We compared richness of amphibians, birds, mammals, reptiles, flowering plants, conifers and cycads, and ferns in all the world's countries. We further tested the effects of mean latitude, altitude span, and insularity on species richness both for all world countries and just for Mediterranean countries. For all taxa and in all tests, Israel lies within the prediction intervals of the models. Out of 42 tests, Israel's residuals lie in the upper decile of positive residuals once: for reptiles, when compared to all world countries, taking all predicting factors into account. Using only countries larger than 1000 km2, Israel was placed as top residual when compared to other Mediterranean countries for mammals and reptiles. We therefore conclude that Israel's species richness does not significantly exceed the expected values for a country its size. This is true when comparing it to either world or just Mediterranean countries. Adding more predicting factors does not change this fact.