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Natural habitats are increasingly affected by anthropogenically driven environmental changes resulting from habitat destruction, chemical and light pollution, and climate change. Organisms inhabiting such habitats are faced with novel disturbances that can alter their modes of signaling. Coloration is one such sensory modality whose production, perception and function is being affected by human-induced disturbances. Animals that acquire pigment derivatives through diet are adversely impacted by the introduction of chemical pollutants into their environments as well as by general loss of natural habitat due to urbanization or logging leading to declines in pigment sources. Those species that do manage to produce color-based signals and displays may face disruptions to their signaling medium in the form of light pollution and turbidity. Furthermore, forest fragmentation and the resulting breaks in canopy cover can expose animals to predation due to the influx of light into previously dark environments. Global climate warming has been decreasing snow cover in arctic regions, causing birds and mammals that undergo seasonal molts to appear conspicuous against a snowless background. Ectotherms that rely on color for thermoregulation are under pressure to change their appearances. Rapid changes in habitat type through severe fire events or coral bleaching also challenge animals to match their backgrounds. Through this review, we aim to describe the wide-ranging impacts of anthropogenic environmental changes on visual ecology and suggest directions for the use of coloration both as an indicator of ecological change and as a tool for conservation.

Objectives Neonates of several primate species are born with very different pelage coloration from their parents but then assume adult coat color within weeks or months of birth. We set out to test the three conventional functional hypotheses for this distinctive transient natal coat coloration in primates (infanticide, allomothering, and confusion of paternity) as well as solicitation of maternal care, and across all neonate primates, background matching, and Gloger's rule (dark coats being associated with humid environments). Materials and Methods To examine the functional significance of neonate pelage coloration, we employed five different measures of distinctive coat coloration, new updated information on primate life histories, and a complete primate phylogeny of 286 species to control for shared ancestry. Results Across primates, we found a strong association between distinctive natal coats and the prevalence of infanticide but no support for allomothering or confusing paternity. We also found that species in which young have distinct natal coats have relatively shorter interbirth intervals, as well as a tendency to be weaned earlier which is unrelated to allomothering. Darker primate natal coats (whether distinctive or not) are not found in shadier, warmer, or wetter habitats. Discussion While distinct natal coats in primates are generally found in infanticidal species, we argue on logical grounds that this is not an advertisement to incoming males but instead neonate coloration solicits greater maternal care. This enables infants to pass through this infanticide-induced mortality-prone infant phase more rapidly. Conspicuous neonate coats in comparison to adults appear to act as a super-normal stimulus for mothers to hasten post-natal development of their offspring.

Of all hypotheses advanced for why zebras have stripes, avoidance ofbiting fly attack receives by far the most support, yet the mechanisms bywhich stripes thwart landings are not yet understood. A logical and popularhypothesis is that stripes interfere with optic flow patterns needed by flyinginsects to execute controlled landings. This could occur through disruptingthe radial symmetry of optic flow via the aperture effect (i.e. generation offalse motion cues by straight edges), or through spatio-temporal aliasing(i.e. misregistration of repeated features) of evenly spaced stripes. By recordingand reconstructing tabanid fly behaviour around horses wearingdifferently patterned rugs, we could tease out these hypotheses using realistictarget stimuli. We found that flies avoided landing on, flew faster near,and did not approach as close to striped and checked rugs compared togrey. Our observations that flies avoided checked patterns in a similarway to stripes refutes the hypothesis that stripes disrupt optic flow via theaperture effect, which critically demands parallel striped patterns. Ourdata narrow the menu of fly-equid visual interactions that form the basisfor the extraordinary coloration of zebras.

Protected areas are the cornerstone of in situ conservation and their effective management is critical for maintaining biodiversity in the long term. In East Africa (Burundi, Kenya, Rwanda, Tanzania and Uganda) there are 1,776 protected areas (including 186 “strict” protected areas with IUCN management categories I through IV) covering more than 27% of its terrestrial area. Here we document the extent to which East African protected areas encompass ecoregions and endemic terrestrial vertebrate taxa, and using new land conversion data derived from medium to high spatial resolution satellite images, we assess how they have been encroached upon by agriculture and other land use. We find that East African protected areas cover 86% of ecoregions well (>10% threshold of ecoregion representativeness set by the Convention on Biological Diversity's Aichi Target 11), some very well (>90% - Rwenzori-Virunga montane moorlands and East African montane moorlands). In contrast, Masai xeric grasslands and shrublands, Somali Acacia-Commiphora bushlands and thickets, and Southern Swahili coastal forests and woodlands are poorly represented. Protected areas cover at least 10% of the distribution of 256 of 303 East African endemic and near-endemic terrestrial vertebrate species (the latter defined here as having 90% or more of their range in East Africa). However, 37% of these species' ranges do not have at least 10% coverage by strict PAs and only 26% of endemic species have at least half of their range covered by PAs. Encouragingly, we find that only 6.8% of East African protected areas has been converted to agriculture or other human use since gazettement. Only 1.6% of strict protected areas have been converted providing very strong evidence that strict protection is the most enduring way of safeguarding habitat. Keywords: Biodiversity, Conservation prioritization, Effectiveness, Endemic species, National parks, Representativeness

Ecological surrogacy – here defined as using a process or element (e.g., species, ecosystem, or abiotic factor) to represent another aspect of an ecological system – is a widely used concept, but many applications of the surrogate concept have been controversial. We argue that some of this controversy reflects differences among users with different goals, a distinction that can be crystalized by recognizing two basic types of surrogate. First, many ecologists and natural resource managers measure “indicator surrogates” to provide information about ecological systems. Second, and often overlooked, are “management surrogates” (e.g., umbrella species) that are primarily used to facilitate achieving management goals, especially broad goals such as “maintain biodiversity” or “increase ecosystem resilience.” We propose that distinguishing these two overarching roles for surrogacy may facilitate better communication about project goals. This is critical when evaluating the usefulness of different surrogates, especially where a potential surrogate might be useful in one role but not another. Our classification for ecological surrogacy applies to species, ecosystems, ecological processes, abiotic factors, and genetics, and thus can provide coherence across a broad range of uses.

Habitat loss and overexploitation are driving differential declines in vertebrate taxa but variation in responses means it is often difficult to determine where to place conservation effort. Here we present an easy-to-use method to rank the relative sensitivities of the larger mammals of savanna Africa to human activities in order to prioritize conservation activities. We first made coarse predictions about susceptibility based on species’ intrinsic ecological traits. Next we determined actual presence of these species using transect surveys within the heavily impacted Wami-Mbiki Wildlife Management Area in Tanzania, by conducting interviews outside this protected area, and monitoring changes in populations within both of these zones. Finally we used these combined data to derive a sensitivity measure that we compared to prior predictions about the susceptibility. Our empirical measure of sensitivity to humans was positively correlated with species’ body mass, and home range size. The empirical data allowed us to categorize these species into those that are very sensitive to humans (species in danger), sensitive to humans (human avoiders), moderately common species (human adapters), and those that are positively impacted by people (human exploiters). Conservation efforts aimed at human avoiders and species in danger are likely to have disproportionate payoffs in protecting larger mammal assemblages in Africa as these more sensitive species likely act as focal species (sensu Lambeck, 1997) for management efforts. Our measures combine easy-to-conduct transect data with interview data, and evaluate temporal changes to reach conclusions about how sensitive large mammals are to humans. These methods can be applied in other regions where studies are beginning to examine wildlife declines outside protected areas.

Habitat fragmentation plays a major role in the reduction of genetic diversity among wildlife populations. The African savannah elephant population of the Ruaha-Rungwa and Katavi-Rukwa ecosystems in south-western Tanzania, comprises one of the world’s largest remaining elephant populations, but is increasingly threatened by loss of connectivity and poaching for ivory. We investigate whether there are incipient signs of genetic isolation (loss of heterozygosity) within the younger cohort as a result of habitat loss between the two ecosystems. To investigate the genetic structure of populations, we compared the genotypes for 11 microsatellite loci in the western (n = 81 individuals from Katavi-Rukwa), central (n = 36 individuals from Lukwati and Piti), and eastern populations (n = 193, individuals from Ruaha-Rungwa). We found evidence of significant genetic differentiation among the three populations, but the levels were low, suggesting recent divergence. Furthermore, we identified weak isolation by distance, suggesting higher gene flow among nearer individuals with samples within 50km of each other being more genetically similar to one another than beyond. Although sample sizes were small, a further analysis of genetic differences across populations and in separate age classes revealed evidence of increasing genetic structure among younger age classes across the landscape. In a long-lived species with overlapping generations, it takes a long time to develop genetic substructure even when there are substantial obstacles to migration. Thus, in these recently fragmented populations, inbreeding (and the loss of heterozygosity) may be less of an immediate concern than demography (the loss of adults due to illegal hunting).

Research on animal coloration is a vibrant area of biology currently involving evolutionary biologists, behavioural ecologists, psychologists, optical physicists, visual ecologists, geneticists and anthropologists. The proliferation of recent work requires that we take stock of the field, aiming to identify major themes, questions and future directions. This was the goal of the year-long Wissenschaftskolleg zu Berlin ‘focus group’ (2015–2016), in which many of the authors in this issue participated either as fellows or visitors. The result is this 19-chapter theme issue, in which we pinpoint the breakthroughs and challenges in animal coloration research, focusing on production, perception, function and evolution. We also explore animal coloration research as it applies to humans. This theme issue is by no means exhaustive but our goal has been to summarize …

Loss of natural landscapes surrounding major conservation areas compromise their future and threaten long-term conservation. We evaluate the effectiveness of fully and lesser protected areas within Katavi-Rukwa and Ruaha-Rungwa ecosystems in south-western Tanzania to protecting natural landscapes within their boundaries over the past four decades. Using a time series of Landsat satellite imageries of September 1972, July 1990 and September 2015, we assess the extent to which natural habitat has been lost within and around these areas mainly through anthropogenic activities. We also test the viability of the remaining natural habitat to provide connectivity between the two ecosystems. Our analysis reveals that while fully protected areas remained intact over the past four decades, lesser protected areas lost a combined total area of about 5,984 km2 during that period which is about 17.5% of habitat available in 1972. We also find that about 3,380 km2 of natural habitat is still available for connectivity between the two ecosystems through Piti East and Rungwa South Open Areas. We recommend relevant authorities to establish conservation friendly village land use plans in all villages surrounding and between the two ecosystems to ensure long-term conservation of these ecosystems.

In living color Animals live in a colorful world, but we rarely stop to think about how this color is produced and perceived, or how it evolved. Cuthill et al. review how color is used for social signals between individual animals and how it affects interactions with parasites, predators, and the physical environment. New approaches are elucidating aspects of animal coloration, from the requirements for complex cognition and perception mechanisms to the evolutionary dynamics surrounding its development and diversification. Science , this issue p. eaan0221

Correspondence Nourish as well as feed the world The report released last week by the Global Panel on Agriculture and Food Systems for Nutrition warns that only a response comparable in scale and commitment to that directed against HIV/AIDS and malaria will be sufficient to meet the challenge of changing food systems (see www.glopan.org/ foresight). Our independent experts used modelling and trend analysis to scrutinize diets and food systems and how these could change by 2030. Three billion people from 193 countries now have poor- quality diets, and populations in nearly half of all countries are increasingly experiencing serious under-nutrition that is coupled with weight gain and obesity. We find that the risk posed by poor diets to mortality and morbidity is now greater than the combined risks of unsafe sex, alcohol, drug and tobacco use. As director of the Global Panel’s secretariat, I have worked closely with the panel in producing this report, which recommends that food systems should be repositioned from feeding people to nourishing them. Action must go beyond agriculture to encompass trade, the environment and health, harnessing the power of the private sector and empowering consumers to demand better diets. Sandy Thomas Global Panel on Agriculture and Food Systems for Nutrition, London. sandy.thomas@glopan.org Species loss: diverse takes on biodiversity Sean Maxwell and colleagues argue that agriculture is one of the greatest enemies of biodiversity — yet agriculture itself depends on biodiversity (Nature 536, 143–145; 2016). To make sense of this, we need to recognize that perspectives on biodiversity can depend on context. The authors are really referring to a limited range of species that are mainly of interest to conservationists, which could be called ‘conservation biodiversity’. The biodiversity that supports global primary food production and a host of other industries, from pharmaceutical bioprospecting and engineering biomimetics to biological pest control (see, for example, go.nature.com/2croaxv), might then be classed as ‘production biodiversity’. Production biodiversity is enormous and irreplaceable. It constitutes at least 90% of all species — predominantly invertebrates (such as pollinators) and microbes. It harbours most of the planet’s chemical, genetic and metabolic diversity. Global assessment of conservation biodiversity is crucial. But it must acknowledge the greater part of biodiversity on which humanity depends, or the very word ‘biodiversity’ risks losing its scientific, economic and social meaning. Andrew Beattie Macquarie University, Sydney, Australia. andrew.beattie@mq.edu.au Species loss: a crude view of climate We contend that Sean Maxwell and colleagues’ analysis of risk factors for biodiversity loss should have included a more nuanced view of climate change (Nature 536, 143–145; 2016) . For example, the authors seem to rely too much on extreme climate hazards in assessing climate threats to biodiversity. They also overlook the fact that the extinction-risk criteria for species on the IUCN Red List often fail to capture risks from climate (see, for example, W. B. Foden et al. PLoS ONE 8, e65427; 2013). They do not consider slow-onset changes, such as habitat-range shifts and ocean acidification, or indirect threats to wildlife, such as human responses to climate-change effects on food security — particularly in poor populations and tropical regions. Maxwell et al. imply that efforts directed against new (climate) and old (historical) threats are mutually exclusive. We find this simplistic and counterproductive: solutions need to be integrative and additive. They should also have accounted for system interactions — threats don’t occur in isolation. In our view, tackling the complexity and uncertainties of climate change calls for new ideas that focus on emerging threats to species. Without these, dedicated conservation interventions will fail over the long term. Nikhil Advani World Wildlife Fund, Washington DC, USA. Susan Evans WWF Canada, Toronto, Canada. Arjette Stevens WWF Netherlands, Zeist, the Netherlands. nikhil.advani@wwfus.org promoting reforestation will result in financial benefits through carbon accreditation. By contrast, there is widespread, illegal hunting of animals in forest patches across the island. Hunted species include tree hyraxes (Dendrohyrax validus), blue duikers (Philantomba monticola), Pemba flying foxes (Pteropus voeltzkowi) and coconut crabs (Birgus latro). Our case study highlights the mismatch between climate- change mitigation and conserving biodiversity in the tropics. Here, effective efforts to protect trees and reduce climate change may result in conserving only an empty forest. Tim Caro, Monique Borgerhoff Mulder University of California, Davis, USA. tmcaro@ucdavis.edu Species loss: climate plan saves only trees Competition over the bandwidths used by mobile phones and time- critical weather transmissions is only part of the story (see Nature 535, 208–209; 2016). In fact, mobile networks are themselves becoming an important tool for monitoring the weather. Because weather conditions reduce the strength of radio signals transmitted by commercial microwave links in cellular networks, they can act as a virtual environmental- monitoring facility. For instance, commercial cellular data are already being used to track precipitation, fog, near-surface moisture (see, for example, N. David et al. Bull. Am. Meteorol. Soc. 96, 1687–1698; 2015) and dew (O. Harel et al. IEEE Sel. Top. Appl. Earth Obs. Remote Sens. 8, 4396–4404; 2015), and to predict floods (a discovery awarded the World Intellectual Property Organization Medal in 2009). Pinhas Alpert, Hagit Messer Tel Aviv University, Israel. Noam David Cornell University, Ithaca, New York, USA. pinhas@post.tau.ac.il We agree that the challenge of protecting biodiversity — to be considered at the upcoming Conference of the Parties to the Convention on Biological Diversity — must not be eclipsed by climate-change concerns (see S. Maxwell et al. Nature 536, 143–145; 2016). These are complementary but separate issues. On Pemba Island, Tanzania, for example, we conducted systematic but open-ended interviews with village environmental committees, male and female focus groups, and randomly selected households in 11 villages, backed up by less- intensive interviews in 18 wards last year (unpublished results). These revealed a general understanding of the dangers of immediate climate change and of the merits of a pending REDD+ programme (Reducing Emissions from Deforestation and Forest Degradation). Local expectations are high that reducing deforestation and Mobile networks aid weather monitoring d e v r e s e r s t h g i r l l A e r u t a N r e g n i r p S f o t r a p d e t i m i L s r e h s i l b u P n a l l i m c a M 2 9 S E P T E M B E R 2 0 1 6 | VO L 5 3 7 | NAT U R E | 6 1 7

The century-old idea that stripes make zebras cryptic to large carnivores has never been examined systematically. We evaluated this hypothesis by passing digital images of zebras through species-specific spatial and colour filters to simulate their appearance for the visual systems of zebras’ primary predators and zebras themselves. We also measured stripe widths and luminance contrast to estimate the maximum distances from which lions, spotted hyaenas, and zebras can resolve stripes. We found that beyond ca. 50 m (daylight) and 30 m (twilight) zebra stripes are difficult for the estimated visual systems of large carnivores to resolve, but not humans. On moonless nights, stripes are difficult for all species to resolve beyond ca. 9 m. In open treeless habitats where zebras spend most time, zebras are as clearly identified by the lion visual system as are similar-sized ungulates, suggesting that stripes cannot confer crypsis by disrupting the zebra’s outline. Stripes confer a minor advantage over solid pelage in masking body shape in woodlands, but the effect is stronger for humans than for predators. Zebras appear to be less able than humans to resolve stripes although they are better than their chief predators. In conclusion, compared to the uniform pelage of other sympatric herbivores it appears highly unlikely that stripes are a form of anti-predator camouflage.

Surrogate concepts are used in all sub-disciplines of environmental science. However, controversy remains regarding the extent to which surrogates are useful for resolving environmental problems. Here, we argue that conflicts about the utility of surrogates (and the related concepts of indicators and proxies) often reflect context-specific differences in trade-offs between measurement accuracy and practical constraints. By examining different approaches for selecting and applying surrogates, we identify five trade-offs that correspond to key points of contention in the application of surrogates. We then present an 8-step Adaptive Surrogacy Framework that incorporates cross-disciplinary perspectives from a wide spectrum of the environmental sciences, aiming to unify surrogate concepts across disciplines and applications. Our synthesis of the science of surrogates is intended as a first step towards fully leveraging knowledge accumulated across disciplines, thus consolidating lessons learned so that they may be accessible to all those operating in different fields, yet facing similar hurdles.

Conservationists often advocate for landscape approaches to wildlife management while others argue for physical separation between protected species and human communities, but direct empirical comparisons of these alternatives are scarce. We relate African lion population densities and population trends to contrasting management practices across 42 sites in 11 countries. Lion populations in fenced reserves are significantly closer to their estimated carrying capacities than unfenced populations. Whereas fenced reserves can maintain lions at 80% of their potential densities on annual management budgets of $500 km(-2) , unfenced populations require budgets in excess of $2000 km(-2) to attain half their potential densities. Lions in fenced reserves are primarily limited by density dependence, but lions in unfenced reserves are highly sensitive to human population densities in surrounding communities, and unfenced populations are frequently subjected to density-independent factors. Nearly half the unfenced lion populations may decline to near extinction over the next 20-40 years.

We combined findings of an avian field survey conducted in 2003 with the efforts of other observers to develop a comprehensive species list for the Katavi-Rukwa ecosystem; a biologically rich area of western Tanzania. Our 2003 survey, during the dry season, yielded 222 species of birds, four of which had not been reported previously. In combination with other publications, field reports, and incidental observations we documented 458 species of birds occurring in this ecosystem. The confirmed presence of ten globally threatened species, 18 biome restricted species, one range restricted species (Tanzanian masked weaver Ploceus reichardi), and significant numbers of African skimmer (Rynchops flavirostris), a colonial waterbird, strongly reinforces the classification of the Katavi National Park as an Important Bird Area in Tanzania. A synopsis of species found in this area supports the view that the avifauna of the Katavi-Rukwa ecosystem is biogeographically affiliated with the Zambezian biome. These findings will provide a baseline for conservation, management, and future biodiversity and avian research efforts in the Katavi-Rukwa ecosystem.

Here I survey, collate and synthesize contrasting coloration in 5000 species of terrestrial mammals focusing on black and white pelage. After briefly reviewing alternative functional hypotheses for coloration in mammals, I examine nine colour patterns and combinations on different areas of the body and for each mammalian taxon to try to identify the most likely evolutionary drivers of contrasting coloration. Aposematism and perhaps conspecific signalling are the most consistent explanations for black and white pelage in mammals; background matching may explain white pelage. Evidence for contrasting coloration is being involved in crypsis through pattern blending, disruptive coloration or serving other functions, such as signalling dominance, lures, reducing eye glare or in temperature regulation has barely moved beyond anecdotal stages of investigation. Sexual dichromatism is limited in this taxon and its basis is unclear. Astonishingly, the functional significance of pelage coloration in most large charismatic black and white mammals that were new to science 150 years ago still remains a mystery.

Strict protectionism, resource extraction, protected-area community outreach, ecotourism, an integrated conservation and development program, comanagement schemes, and citizen-science initiatives are all being used to help conserve the remote Katavi-Rukwa ecosystem in western Tanzania. Biological and social research show that protectionism is successful in the conservation of large mammals but fails to capture diverse species communities; extractivism is appropriate for some resources but not for others; protected-area outreach can be effective for some communities; and devolved control over wildlife, in conjunction with ecotourism and citizen science, has considerable potential in the area. The long-term nature of the research provides the necessary time frame to evaluate outcomes of different conservation strategies, uncovers dynamics within communities that affect attitudes and responses to conservation initiatives, provides impartial recommendations because changing research personnel offers different viewpoints, and, probably most importantly, enhances trust among stakeholders. Currently, there are limited institutional mechanisms for ensuring the input of biological and social science in shaping conservation practice in Tanzania, and long-term research can help informally bridge the gap.

The natural occurrence of lentiviruses closely related to feline immunodeficiency virus (FIV) in nondomestic felid species is shown here to be worldwide. Cross-reactive antibodies to FIV were common in several free-ranging populations of large cats, including East African lions and cheetahs of the Serengeti ecosystem and in puma (also called cougar or mountain lion) populations throughout North America. Infectious puma lentivirus (PLV) was isolated from several Florida panthers, a severely endangered relict puma subspecies inhabiting the Big Cypress Swamp and Everglades ecosystems in southern Florida. Phylogenetic analysis of PLV genomic sequences from disparate geographic isolates revealed appreciable divergence from domestic cat FIV sequences as well as between PLV sequences found in different North American locales. The level of sequence divergence between PLV and FIV was greater than the level of divergence between human and certain simian immunodeficiency viruses, suggesting that the transmission of FIV between feline species is infrequent and parallels in time the emergence of HIV from simian ancestors.