Lemur Gut Microeukaryotic Community Variation Is Not Associated with Host Phylogeny, Diet, or Habitat

Identifying the major forces driving variation in gut microbiomes enhances our understanding of how and why symbioses between hosts and microbes evolved. Gut prokaryotic community variation is often closely associated with host evolutionary and ecological variables. Whether these same factors drive variation in other microbial taxa occupying the animal gut remains largely untested. Here, we present a one-to-one comparison of gut prokaryotic (16S rRNA metabarcoding) and microeukaryotic (18S rRNA metabarcoding) community patterning among 12 species of wild lemurs. Lemurs were sampled from dry forests and rainforests of southeastern Madagascar and display a range of phylogenetic and ecological niche diversity. We found that while lemur gut prokaryotic community diversity and composition vary with host taxonomy, diet, and habitat, gut microeukaryotic communities have no detectable association with any of these factors. We conclude that gut microeukaryotic community composition is largely random, while gut prokaryotic communities are conserved among host species. It is likely that a greater proportion of gut microeukaryotic communities comprise taxa with commensal, transient, and/or parasitic symbioses compared with gut prokaryotes, many of which form long-term relationships with the host and perform important biological functions. Our study highlights the importance of greater specificity in microbiome research; the gut microbiome contains many "omes" (e.g., prokaryome, eukaryome), each comprising different microbial taxa shaped by unique selective pressures.

A Nuanced Examination of Primate Capture and Consumption and Human Socio-Economic Well-Being in Kirindy Mitea National Park, Madagascar

The futures of human and nonhuman primates are closely tied in protected areas. Understanding this interconnectedness is especially urgent in Madagascar, one of the world's most impoverished biodiversity hotspots. Yet, no study has evaluated the relationship between poverty and lemur hunting and consumption using a composite poverty metric that includes health, education, and living standards. To address this gap, and to inform primate conservation practice and policy, we administered annual surveys to 81 households over six consecutive months (September 2018 to March 2019) in a village on the border of Kirindy Mitea National Park, Madagascar. We observed extreme deprivation scores across multiple dimensions of poverty and identified ninety-five percent of households as 'impoverished'. Of these, three-quarters (77%) of households were identified as being in 'severe poverty'. One-fifth (19%) of all households hunted lemurs and half (49%) of households consumed lemurs. While poverty eradication is an urgent need in communities around Kirindy Mitea National Park, our findings show no relationship between poverty and lemur hunting and consumption, perhaps due to the lack of variance in poverty. Our results highlight the need to investigate other contributory factors to lemur hunting and consumption locally. Because food insecurity is a known driver of lemur hunting and consumption among the study community, and because domestic meats can be preferred over protected species, we recommend testing the efficacy of livestock interventions near Kirindy Mitea National Park.

Updated lemur species ranges in Madagascar's Corridor Forestier d'Ambositra Vondrozo (COFAV)

Madagascar's high rates of endemism, paired with its escalating deforestation rates, has made it one of the most important conservation priorities on the planet. In southeastern Madagascar, the Corridor Forestier d'Ambositra Vondrozo (COFAV) is an unprotected rainforest corridor that sustains ∼15 species of lemurs, most of which are endangered. The COFAV connects many protected areas and is therefore essential for gene flow, dispersal, and the long-term sustainability of animal populations in the area. The corridor has not been surveyed extensively since the 1990s, and even so, only a fraction of the sites have been sampled multiple times. The goal of our study was to survey the COFAV, from Ranomafana National Park to the Mananara River, to provide updated species occurrences and ranges. Combining data across multiple teams using different inventorying methods, we surveyed a total area of 227 km2 throughout an eight-month period. We recorded every lemur occurrence (sighting or vocalization) and noted the species, date, time, group size, and GPS coordinates. We found 11 lemur species and one putative hybrid species. The geographic ranges for three species (Hapalemur aureus, H. griseus, Propithecus edwardsi) were larger than previously thought. The range of Varecia variegata should be shortened and adjusted accordingly, as the species appears transient (at best) in the northern parts of Ranomafana National Park and was not found south of the Ambohimahamasina/Ikongo region. This study provides updated geographic ranges for lemur species in the COFAV, important information for future censuses, species assessments, and conservation measures for future implementation.

An overdue catalyst: Limitations imposed by COVID-19 improved capacity building in community-led environmental education in Madagascar

The COVID-19 pandemic caused by the SARS-CoV-2 virus brought many primatology research programs and conservation efforts to a halt. After Madagascar closed its borders during March 2020, many on-site international project leaders and researchers returned to their home countries when their programs were delayed or canceled. Madagascar remained closed to travelers until November 2021, when it reopened to international flights. The 20-month absence of international researchers allowed many local Malagasy program staff, wildlife professionals, and community leaders to step into new leadership roles and responsibilities. Many programs that already had strong Malagasy leadership and meaningful collaborations with local communities flourished, while others either swiftly strengthened these attributes or faced challenges from pandemic-related travel restrictions. Here, we describe how the coronavirus pandemic events of 2020-2021 initiated long-overdue shifts in outdated models of internationally led primate research and education projects in communities living alongside primates at risk of extinction. We discuss the benefits and challenges of pandemic-induced changes within five primatological outreach projects, as well as how we can use these experiences to improve community-led environmental education and conservation awareness in the future.

Evaluating the impact of environmental education around Ranomafana National Park

A total of 94% of lemur species are currently threatened with extinction and more than 17 species of giant lemur are already extinct. To help prevent the extinction of Madagascar's remaining lemurs, Dr. Patricia Wright initiated conservation programs in the Ranomafana region of southern Madagascar in the 1990s. These continued and expanded, and in 2003 were consolidated with Dr. Wright's research activities when Center ValBio ("CVB") was founded in 2003. CVB believes in the "One Health" approach in understanding the relationship between humans and the environment, and one of their core principles is that effective conservation is science-based. CVB's environmental education (EE) programs (discussed herein) operate in various primary schools surrounding Ranomafana national park (RNP). The all-Malagasy team consists of long-term conservation educators as well as young intern teachers, who together address the issues of valuing lemurs and the forests that they require to survive. In this paper, we will describe three of CVB's EE programs and evaluate their impact. The primary tool used to assess impact was an analysis of pre- and post -intervention test scores evaluated using a Kruskal-Wallis test. We show that these programs (1) are popular, (2) produce concrete outputs that can change rural villages, and (3) improve local knowledge on the importance of biodiversity and sustainable development.

Significant effects of host dietary guild and phylogeny in wild lemur gut microbiomes

Mammals harbor diverse gut microbiomes (GMs) that perform critical functions for host health and fitness. Identifying factors associated with GM variation can help illuminate the role of microbial symbionts in mediating host ecological interactions and evolutionary processes, including diversification and adaptation. Many mammals demonstrate phylosymbiosis-a pattern in which more closely-related species harbor more similar GMs-while others show overwhelming influences of diet and habitat. Here, we generated 16S rRNA sequence data from fecal samples of 15 species of wild lemurs across southern Madagascar to (1) test a hypothesis of phylosymbiosis, and (2) test trait correlations between dietary guild, habitat, and GM diversity. Our results provide strong evidence of phylosymbiosis, though some closely-related species with substantial ecological niche overlap exhibited greater GM similarity than expected under Brownian motion. Phylogenetic regressions also showed a significant correlation between dietary guild and UniFrac diversity, but not Bray-Curtis or Jaccard. This discrepancy between beta diversity metrics suggests that older microbial clades have stronger associations with diet than younger clades, as UniFrac weights older clades more heavily. We conclude that GM diversity is predominantly shaped by host phylogeny, and that microbes associated with diet were likely acquired before evolutionary radiations within the lemur families examined.

Madagascar Terrestrial Camera Survey Database 2021: A collation of protected forest camera surveys from 2007-2021

Madagascar is a threatened global biodiversity hotspot and conservation priority, yet we lack broadscale surveys to assess biodiversity across space and time. To fill this gap, we collated camera trap surveys, capturing species occurrences within Madagascar into a single standardized database. This dataset includes nine distinct protected areas of Madagascar and encompasses 13 subprojects, 38 camera arrays, 1156 sampling units (independent camera site per survey) within two important biodiversity eco-regions: western dry deciduous forest, and eastern humid rainforest. Camera surveys were conducted from June 2007 to January 2021. The final dataset includes 17 unique families of mammals (Bovidae, Canidae, Cheirogaleidae, Daubentoniidae, Equidae, Eupleridae, Felidae, Hominidae, Indriidae, Lemuridae, Lepilemuridae, Muridae, Nesomyidae, Pteropodidae, Soricidae, Suidae, Tenrecidae)comprising 45 species and 27 unique families of birds (Accipitridae, Acrocephalidae, Alcedinidae, Bernieridae, Brachypteraciidae, Caprimulgidae, Cisticolidae, Columbidae, Coraciidae, Corvidae, Cuculidae, Dicruridae, Mesitornithidae, Monarchidae, Motacillidae, Muscicapidae, Numididae, Phasianidae, Rallidae, Sarothruridae, Strigidae, Sturnidae, Sulidae, Threskiornithidae, Upupidae, Vangidae, Zosteropidae) comprising 58 species. Images were processed and verified by individual project dataset creators and camera operation and species tables were then collated. The final product represents the first broad-scale freely available standardized formal faunal database for Madagascar. Data are available through this publication and at DOI:10.5281/zenodo.5801806. These data will be useful for examining species- and community- level trends in occurrence across space or time within Madagascar and globally, evaluating native and invasive species dynamics, and aid in determining species conservation status and planning for at-risk species. There are no copyright restrictions; please cite this paper when using the data for publication.

Integrating Health Systems and Science to Respond to COVID-19 in a Model District of Rural Madagascar

There are many outstanding questions about how to control the global COVID-19 pandemic. The information void has been especially stark in the World Health Organization Africa Region, which has low per capita reported cases, low testing rates, low access to therapeutic drugs, and has the longest wait for vaccines. As with all disease, the central challenge in responding to COVID-19 is that it requires integrating complex health systems that incorporate prevention, testing, front line health care, and reliable data to inform policies and their implementation within a relevant timeframe. It requires that the population can rely on the health system, and decision-makers can rely on the data. To understand the process and challenges of such an integrated response in an under-resourced rural African setting, we present the COVID-19 strategy in Ifanadiana District, where a partnership between Malagasy Ministry of Public Health (MoPH) and non-governmental organizations integrates prevention, diagnosis, surveillance, and treatment, in the context of a model health system. These efforts touch every level of the health system in the district-community, primary care centers, hospital-including the establishment of the only RT-PCR lab for SARS-CoV-2 testing outside of the capital. Starting in March of 2021, a second wave of COVID-19 occurred in Madagascar, but there remain fewer cases in Ifanadiana than for many other diseases (e.g., malaria). At the Ifanadiana District Hospital, there have been two deaths that are officially attributed to COVID-19. Here, we describe the main components and challenges of this integrated response, the broad epidemiological contours of the epidemic, and how complex data sources can be developed to address many questions of COVID-19 science. Because of data limitations, it still remains unclear how this epidemic will affect rural areas of Madagascar and other developing countries where health system utilization is relatively low and there is limited capacity to diagnose and treat COVID-19 patients. Widespread population based seroprevalence studies are being implemented in Ifanadiana to inform the COVID-19 response strategy as health systems must simultaneously manage perennial and endemic disease threats.

Quantitative proteomic comparison of salt stress in Chlamydomonas reinhardtii and the snow alga Chlamydomonas nivalis reveals mechanisms for salt-triggered fatty acid accumulation via reallocation of carbon resources

BACKGROUND

Chlamydomonas reinhardtii is a model green alga strain for molecular studies; its fully sequenced genome has enabled omic-based analyses that have been applied to better understand its metabolic responses to stress. Here, we characterised physiological and proteomic changes between a low-starch C. reinhardtii strain and the snow alga Chlamydomonas nivalis, to reveal insights into their contrasting responses to salinity stress.

RESULTS

Each strain was grown in conditions tailored to their growth requirements to encourage maximal fatty acid (as a proxy measure of lipid) production, with internal controls to allow comparison points. In 0.2 M NaCl, C. nivalis accumulates carbohydrates up to 10.4% DCW at 80 h, and fatty acids up to 52.0% dry cell weight (DCW) over 12 days, however, C. reinhardtii does not show fatty acid accumulation over time, and shows limited carbohydrate accumulation up to 5.5% DCW. Analysis of the C. nivalis fatty acid profiles showed that salt stress improved the biofuel qualities over time. Photosynthesis and respiration rates are reduced in C. reinhardtii relative to C. nivalis in response to 0.2 M NaCl. De novo sequencing and homology matching was used in conjunction with iTRAQ-based quantitative analysis to identify and relatively quantify proteomic alterations in cells exposed to salt stress. There were abundance differences in proteins associated with stress, photosynthesis, carbohydrate and lipid metabolism proteins. In terms of lipid synthesis, salt stress induced an increase in dihydrolipoyl dehydrogenase in C. nivalis (1.1-fold change), whilst levels in C. reinhardtii remained unaffected; this enzyme is involved in acetyl CoA production and has been linked to TAG accumulation in microalgae. In salt-stressed C. nivalis there were decreases in the abundance of UDP-sulfoquinovose (- 1.77-fold change), which is involved in sulfoquinovosyl diacylglycerol metabolism, and in citrate synthase (- 2.7-fold change), also involved in the TCA cycle. Decreases in these enzymes have been shown to lead to increased TAG production as fatty acid biosynthesis is favoured. Data are available via ProteomeXchange with identifier PXD018148.

CONCLUSIONS

These differences in protein abundance have given greater understanding of the mechanism by which salt stress promotes fatty acid accumulation in the un-sequenced microalga C. nivalis as it switches to a non-growth state, whereas C. reinhardtii does not have this response.

Exploratory analysis reveals arthropod consumption in 10 lemur species using DNA metabarcoding

Arthropods (insects, spiders, etc.) can fulfill major nutritional requirements for primates, particularly in terms of proteins, fats, vitamins, and minerals. Yet, for many primate species we know very little about the frequency and importance of arthropod consumption. Traditional methods for arthropod prey identification, such as behavioral observations and fecal dissections, offer limited taxonomic resolution and, as a result, underestimate true diversity. Metabarcoding arthropod DNA from primate fecal samples provides a promising but underused alternative. Here, we inventoried arthropod prey diversity in wild lemurs by sequencing two regions of the CO1 gene. Samples were collected opportunistically from 10 species of lemurs inhabiting three national parks in southern Madagascar using a combination of focal animal follows and live trapping. In total, we detected arthropod DNA in 98 of the 170 fecal samples analyzed. Although all lemur species included in these analyses showed evidence of arthropod consumption, those within the family Cheirogaleidae appeared to consume the highest frequency and diversity of arthropods. To our knowledge, this study presents the first evidence of arthropod consumption in Phaner pallescens, Avahi peyrierasi, and Propithecus verreauxi, and identifies 32 families of arthropods as probable food items that have not been published as lemur dietary items to date. Our study emphasizes the importance of arthropods as a nutritional source and the role DNA metabarcoding can play in elucidating an animal's diet.

Population Estimates of Hubbard's Sportive Lemur (Lepilemur hubbardorum) at Zombitse-Vohibasia National Park, Madagascar

Estimates of population size are fundamental to setting conservation priorities for threatened primate species. Many taxa in the lemur genus Lepilemur remain understudied, and basic population statistics are often dated, incomplete, or absent. Hubbard's sportive lemur (Lepilemur hubbardorum) is known only from the Zombitse-Vohibasia National Park region in southwestern Madagascar. It is listed as Endangered by the IUCN owing to its fragmented, declining habitat and limited geographic range. However, this classification has not been confirmed through systematic population estimates. To address this issue, we undertook line transect surveys in the Zombitse parcel of the National Park. We applied geospatial analyses and data to quantify forest area as a proxy for L. hubbardorumhabitat. We recorded a total of 234 L. hubbardorum sightings over 18 survey nights, representing 47.2 km of survey effort. Our surveys revealed population densities of 145.6 L. hubbardorum individuals per km2 (95% CI: 97.2-218.1), for an extrapolated abundance estimate of ca. 16,500-18,000 L. hubbardorum individuals across the protected forests of the Zombitse parcel. This abundance estimate should be considered provisional, however, because our restricted sampling area did not include the more remote regions of the National Park where habitat disturbance and hunting practices have likely contributed to localized population declines.

Trends in forest fragment research in Madagascar: Documented responses by lemurs and other taxa

The rise in research investigating fragmentation and its impact on primates and other taxa reflects the growing presence of fragmented landscapes themselves. Although numerous studies report the negative effects of fragmentation on biodiversity, it is difficult to generalize responses to fragmentation for specific taxonomic groups, such as non-human primates, when studies have not employed a definitive concept of fragmentation or fragments themselves. Madagascar's high degree of fragmentation, wealth of endemic taxa, and extensive history of ecological research provide the opportunity to compare fragmentation studies across similar contexts. We conducted a literature search of peer-reviewed articles on fragmentation in Madagascar to characterize its trends. A total of 70 articles, 46 of which concentrated on lemurs, tested the impacts of fragmentation on Malagasy taxa, while additional sources conducted research in one or more fragments without testing its effects (n = 112 total, 79 on lemurs). Studies on lemurs most frequently tested fragmentation's impacts on genetics and biodiversity metrics (n = 16 and 15 studies, respectively), although health, modeling, behavioral, and cross-disciplinary techniques were also reported. Responses to fragmentation were reported for 49 lemur species, with most studies concentrated in eastern Madagascar (87%). Although there was variation in the metrics reported in studies testing the effects of fragmentation on Malagasy species, the most common measures were fragment area, isolation, or comparison to a control site. Landscape-scale approaches and examination of fragmentation per se were rarely employed. Characterizing trends of fragmentation research in Madagascar emphasizes the challenges of documenting fragmentation's effects while highlighting the benefits of research within fragmented landscapes, particularly when combined with consideration for how the matrix within human-modified landscapes may impact primate populations.

Variations in the microbiome due to storage preservatives are not large enough to obscure variations due to factors such as host population, host species, body site, and captivity

The study of the primate microbiome is critical in understanding the role of the microbial community in the host organism. To be able to isolate the main factors responsible for the differences observed in microbiomes within and between individuals, confounding factors due to technical variations need to be removed. To determine whether alterations due to preservatives outweigh differences due to factors such as host population, host species, body site, and habitat, we tested three methods (no preservative, 96% ethanol, and RNAlater) for preserving wild chimpanzee (fecal), wild lemur (fecal), wild vervet monkey (rectal, oral, nasal, otic, vaginal, and penile), and captive vervet monkey (rectal) samples. All samples were stored below - 20°C (short term) at the end of the field day and then at - 80°C until DNA extraction. Using 16S rRNA gene sequencing, we show a significant preservative effect on microbiota composition and diversity. Samples stored in ethanol and RNAlater appear to be less different compared with samples not stored in any preservative (none). Our differential analysis revealed significantly higher amounts of Enterococcaceae and Family XI in no preservative samples, Prevotellaceae and Spirochaetaceae in ethanol and RNAlater preserved samples, Oligosphaeraceae in ethanol-preserved samples, and Defluviitaleaceae in RNAlater preserved samples. While these preservative effects on the microbiome are not large enough to remove or outweigh the differences arising from biological factors (e.g., host species, body site, and habitat differences) they may promote misleading interpretations if they have large enough effect sizes compared to the biological factors (e.g., host population).

Local habitat, not phylogenetic relatedness, predicts gut microbiota better within folivorous than frugivorous lemur lineages

Both host phylogenetic placement and feeding strategy influence the structure of the gut microbiome (GMB); however, parsing their relative contributions presents a challenge. To meet this challenge, we compared GMB structure in two genera of lemurs characterized by different dietary specializations, the frugivorous brown lemurs ( Eulemur spp.) and the folivorous sifakas ( Propithecus spp.). These genera sympatrically occupy similar habitats (dry forests and rainforests) and diverged over similar evolutionary timescales. We collected fresh faeces from 12 species (six per host genus), at seven sites across Madagascar, and sequenced the 16S rRNA gene to determine GMB membership, diversity and variability. The lemurs' GMBs clustered predominantly by host genus; nevertheless, within genera, host relatedness did not predict GMB distance between species. The GMBs of brown lemurs had greater evenness and diversity, but were more homogeneous across species, whereas the GMBs of sifakas were differentiated between habitats. Thus, over relatively shallow timescales, environmental factors can override the influence of host phylogenetic placement on GMB phylogenetic composition. Moreover, feeding strategy can underlie the relative strength of host-microbiome coadaptation, with Madagascar's folivores perhaps requiring locally adapted GMBs to facilitate their highly specialized diets.

Perceptions of drones, digital adherence monitoring technologies and educational videos for tuberculosis control in remote Madagascar: a mixed-method study protocol

INTRODUCTION

Poor road and communication infrastructure pose major challenges to tuberculosis (TB) control in many regions of the world. TB surveillance and patient support often fall to community health workers (CHWs) who may lack the time or knowledge needed for this work. To meet the End TB Strategy goal of reducing TB incidence by 90% by 2035, the WHO calls for intensified research and innovation including the rapid uptake of new tools, interventions and strategies. Technologies that 'leapfrog' infrastructure challenges and support CHWs in TB control responsibilities have the potential to dramatically change TB outcomes in remote regions. Such technologies may strengthen TB control activities within challenged national tuberculosis treatment and control programmes (NTPs), and be adapted to address other public health challenges. The deployment of innovative technologies needs to be differentially adapted to context-specific factors. The Drone Observed Therapy System (DrOTS) project was launched in Madagascar in 2017 and integrates a bundle of innovative technologies including drones, digital adherence monitoring technology and mobile device-based educational videos to support TB control.

METHODS AND ANALYSIS

This mixed-methods study gathers and analyses cultural perceptions of the DrOTS project among key stakeholders: patients, community members, CHWs, village chiefs and NTP-DrOTS mobile health teams. Data from questionnaires, semistructured interviews, focus group discussions (FGD) and ethnographic observation gathered from June 2018 to June 2019 are thematically analysed and compared to identify patterns and singularities in how DrOTS stakeholders perceive and interact with DrOTS technologies, its enrolment processes, objectives and team.

ETHICS AND DISSEMINATION

Ethics approval was obtained from the National Bioethics Research Committee of Madagascar and Stony Brook University institutional review board. Study results will be submitted for peer-reviewed publication. In Madagascar, results will be presented in person to Ministry and other Malagasy decision-makers through the Institut Pasteur de Madagascar.

PATIENT AND PUBLIC INVOLVEMENT

This study is designed to foreground the voices of patients and potential patients in the DrOTS programme. CHW participants in this study also supported the design of study information sessions and recruitment strategies. One member of the mobile health team provided detailed input on the wording and content of FGD and interview guides. Study findings will be presented via a report in French and Malagasy to CHW, mobile health team and other village-level participants who have email/internet access.

Effect of socio-ecological factors and parasite infection on body condition of Brown Mouse Lemur Microcebus rufus (Mammalia: Primates: Cheirogaleidae)

Various studies in ecology have shown the relationship between body condition and parasitic loads in nonhuman primates, however, little information is available regarding prosimians such as lemurs.  In this study, the synergistic effect of parasite infection and socio-ecological factors on the body condition of Microcebus rufus in the family Cheirogaleidae was analyzed in Ranomafana National Park in southeastern Madagascar.  This lemur species is characterized by its ability to adapt to different types of forest, and by seasonal fattening.  Based on the factors considered, this species is, therefore, a good model for the study of body condition and ecology of infectious diseases in lemurs. Floatation and direct observation techniques were used for examination of parasite infection.  Two indices considering body condition were analyzed: volume index (VI) and condition index (CI), the residual between the mass observed and the corrected mass.  The generalized linear mixed model (GLMM) was used to model the synergistic effect of parasite infections and socio-ecological factors on variation in body condition, with the identity of individuals used as a random factor.  We identified five species of helminths, one species of protist, and one species of lice which infected the 204 mouse lemurs captured.  There was a sexual difference for all measures of the parasite infection.  The more parasite species an individual was infected with, the smaller was its body size according to the Volume Index that reflects deposits of subcutaneous fat.  Individuals with more positive Condition Index values, particularly females, excreted more parasite eggs or oocyst in their faecal matter.  The results suggest that an individual’s body condition constitutes an indicator of risk of parasite infection and transmission. 

Early Holocene human presence in Madagascar evidenced by exploitation of avian megafauna

Previous research suggests that people first arrived on Madagascar by ~2500 years before present (years B.P.). This hypothesis is consistent with butchery marks on extinct lemur bones from ~2400 years B.P. and perhaps with archaeological evidence of human presence from ~4000 years B.P. We report >10,500-year-old human-modified bones for the extinct elephant birds Aepyornis and Mullerornis, which show perimortem chop marks, cut marks, and depression fractures consistent with immobilization and dismemberment. Our evidence for anthropogenic perimortem modification of directly dated bones represents the earliest indication of humans in Madagascar, predating all other archaeological and genetic evidence by >6000 years and changing our understanding of the history of human colonization of Madagascar. This revision of Madagascar's prehistory suggests prolonged human-faunal coexistence with limited biodiversity loss.

Novel opsin gene variation in large-bodied, diurnal lemurs

Some primate populations include both trichromatic and dichromatic (red-green colour blind) individuals due to allelic variation at the X-linked opsin locus. This polymorphic trichromacy is well described in day-active New World monkeys. Less is known about colour vision in Malagasy lemurs, but, unlike New World monkeys, only some day-active lemurs are polymorphic, while others are dichromatic. The evolutionary pressures underlying these differences in lemurs are unknown, but aspects of species ecology, including variation in activity pattern, are hypothesized to play a role. Limited data on X-linked opsin variation in lemurs make such hypotheses difficult to evaluate. We provide the first detailed examination of X-linked opsin variation across a lemur clade (Indriidae). We sequenced the X-linked opsin in the most strictly diurnal and largest extant lemur, Indri indri, and nine species of smaller, generally diurnal indriids (Propithecus). Although nocturnal Avahi (sister taxon to Propithecus) lacks a polymorphism, at least eight species of diurnal indriids have two or more X-linked opsin alleles. Four rainforest-living taxa-I. indri and the three largest Propithecus species-have alleles not previously documented in lemurs. Moreover, we identified at least three opsin alleles in Indri with peak spectral sensitivities similar to some New World monkeys.

Entamoeba histolytica infection in wild lemurs associated with proximity to humans

Amoebiasis, caused by Entamoeba histolytica, affects 50 million people worldwide, and results in 100,000 deaths annually. It is particularly prevalent in developing nations where poverty and poor sanitation contribute to contamination of food and water. E. histolytica is also a zoonotic protozoan parasite with the potential to infect non-human primates. Lemurs, primates endemic to Madagascar, are the most threatened mammalian group in the world due to habitat loss. As forests disappear, humans and lemurs come into more frequent contact, and the potential for E. histolytica to infect lemurs intensifies. Consequently, we screened 176 fecal samples from seven lemur species at eight sites in the rain forests of southeastern Madagascar for E. histolytica to determine if human proximity influenced lemur infection. Of samples examined, 4.0% (from three lemur species) were positive for E. histolytica. Of lemurs infected with E. histolytica, three (43%) exhibited diarrheal feces. Distance to human settlements explained the variation in E. histolytica infection seen in lemurs. These results provide the first evidence of E. histolytica in wild lemurs and highlight the need for additional work to better understand the eco-epidemiology of this potential threat to these species.

Feeding Ecology and Morphology Make a Bamboo Specialist Vulnerable to Climate Change

Animals with dietary specializations can be used to link climate to specific ecological drivers of endangerment. Only two mammals, the giant panda (Ailuropoda melanoleuca) in Asia and the greater bamboo lemur (Prolemur simus) in Madagascar, consume the nutritionally poor and mechanically challenging culm or trunk of woody bamboos [1-3]. Even though the greater bamboo lemur is critically endangered, paleontological evidence shows that it was once broadly distributed [4, 5]. Here, integrating morphological, paleontological, and ecological evidence, we project the effects of climate change on greater bamboo lemurs. Both the giant panda and the greater bamboo lemur are shown to share diagnostic dental features indicative of a bamboo diet, thereby providing an ecometric indicator [6, 7] of diet preserved in the fossil record. Analyses of bamboo feeding in living populations show that bamboo culm is consumed only during the dry season and that the greater bamboo lemur is currently found in regions with the shortest dry season. In contrast, paleontological localities of the greater bamboo lemurs have the longest dry seasons. Future projections show that many present-day greater bamboo lemur populations will experience prolonged dry seasons similar to those of the localities where only fossils of the greater bamboo lemur are found. Whereas abundant foods such as bamboo allow feeding specialists to thrive, even a moderate change in seasonality may outstrip the capacity of greater bamboo lemurs to persist on their mechanically demanding food source. Coupling known changes in species distribution with high-resolution ecological and historical data helps to identify extinction risks.

The importance of protein in leaf selection of folivorous primates

Protein limitation has been considered a key factor in hypotheses on the evolution of life history and animal communities, suggesting that animals should prioritize protein in their food choice. This contrasts with the limited support that food selection studies have provided for such a priority in nonhuman primates, particularly for folivores. Here, we suggest that this discrepancy can be resolved if folivores only need to select for high protein leaves when average protein concentration in the habitat is low. To test the prediction, we applied meta-analyses to analyze published and unpublished results of food selection for protein and fiber concentrations from 24 studies (some with multiple species) of folivorous primates. To counter potential methodological flaws, we differentiated between methods analyzing total nitrogen and soluble protein concentrations. We used a meta-analysis to test for the effect of protein on food selection by primates and found a significant effect of soluble protein concentrations, but a non-significant effect for total nitrogen. Furthermore, selection for soluble protein was reinforced in forests where protein was less available. Selection for low fiber content was significant but unrelated to the fiber concentrations in representative leaf samples of a given forest. There was no relationship (either negative or positive) between the concentration of protein and fiber in the food or in representative samples of leaves. Overall our study suggests that protein selection is influenced by the protein availability in the environment, explaining the sometimes contradictory results in previous studies on protein selection. Am. J. Primatol. 79:e22550, 2017. © 2016 Wiley Periodicals, Inc.

Small-scale land-use variability affects Anopheles spp. distribution and concomitant Plasmodium infection in humans and mosquito vectors in southeastern Madagascar

Background

Deforestation and land-use change have the potential to alter human exposure to malaria. A large percentage of Madagascar’s original forest cover has been lost to slash-and-burn agriculture, and malaria is one of the top causes of mortality on the island. In this study, the influence of land-use on the distribution of Plasmodium vectors and concomitant Plasmodium infection in humans and mosquito vectors was examined in the southeastern rainforests of Madagascar.

Methods

From June to August 2013, health assessments were conducted on individuals living in sixty randomly selected households in six villages bordering Ranomafana National Park. Humans were screened for malaria using species-specific rapid diagnostic tests (RDTs), and surveyed about insecticide-treated bed net (ITN) usage. Concurrently, mosquitoes were captured in villages and associated forest and agricultural sites. All captured female Anopheline mosquitoes were screened for Plasmodium spp. using a circumsporozoite enzyme-linked immunosorbent assay (csELISA).

Results

Anopheles spp. dominated the mosquito communities of agricultural and village land-use sites, accounting for 41.4 and 31.4 % of mosquitoes captured respectively, whereas Anopheles spp. accounted for only 1.6 % of mosquitoes captured from forest sites. Interestingly, most Anopheles spp. (67.7 %) were captured in agricultural sites in close proximity to animal pens, and 90.8 % of Anopheles mosquitoes captured in agricultural sites were known vectors of malaria. Three Anopheline mosquitoes (0.7 %) were positive for malaria (Plasmodium vivax-210) and all positive mosquitoes were collected from agricultural or village land-use sites. Ten humans (3.7 %) tested were positive for P. falciparum, and 23.3 % of those surveyed reported never sleeping under ITNs.

Conclusions

This study presents the first report of malaria surveillance in humans and the environment in southeastern Madagascar. These findings suggest that even during the winter, malaria species are present in both humans and mosquitoes; with P. falciparum found in humans, and evidence of P. vivax-210 in mosquito vectors. The presence of P. vivax in resident vectors, but not humans may relate to the high incidence of humans lacking the Duffy protein. The majority of mosquito vectors were found in agricultural land-use sites, in particular near livestock pens. These findings have the potential to inform and improve targeted malaria control and prevention strategies in the region.

Electronic supplementary material

The online version of this article (doi:10.1186/s12936-016-1164-2) contains supplementary material, which is available to authorized users.

Field evaluation of synthetic lure (3-methyl-1-butanol) when compared to non odor-baited control in capturing Anopheles mosquitoes in varying land-use sites in Madagascar

BACKGROUND

Malaria is the 4(th) largest cause of mortality in Madagascar. To better understand malaria transmission dynamics, it is crucial to map the distribution of the malaria vectors, mosquitoes belonging to the genus Anopheles. To do so, it is important to have a strong Anopheles-specific lure to ensure the maximum number of captures. Previous studies have isolated volatiles from the human skin microbiota and found the compound 3-methyl-1-butanol to be the most attractive to the malaria mosquito, Anopheles gambiae, in a laboratory setting; and recommended 3-methyl-1-butanol as a compound to increase An. gambiae captures in the field. To date, this compound's ability to lure wild mosquitoes in differing land-use settings has not been tested. In this study, we evaluate the role of the synthetic compound, 3-methyl-1-butanol in combination with field produced CO(2) in attracting Anopheles mosquitoes in varying land-use sites in Madagascar.

METHODS

CDC miniature light traps in combination with field produced CO(2) were deployed in and around six villages near Ranomafana National Park, Madagascar. To test the role of 3-methyl-1-butanol in luring Anopheles mosquitoes, two traps were set in each land-use site (village, agricultural sites, and forested habitats affiliated with each village). One was baited with the synthetic odor and the other was kept as a non-baited control.

RESULTS

While 3-methyl-1-butanol baited traps did capture An. gambiae s.l. in this study, we did not find traps baited with synthetic 3-methyl-1-butanol to be more successful in capturing Anopheles mosquitoes, (including Anopheles gambiae s.l.) than the non odor-baited control traps in any of the land-use sites examined; however, regardless of odor bait, trapping near livestock pens resulted in the capture of significantly more Anopheles specimens.

CONCLUSIONS

A strong synthetic lure in combination with insecticide has great potential as a mosquito control. Our findings suggest that trapping mosquitoes near livestock in malaria endemic regions, such as Madagascar, may be more successful at capturing Anopheles mosquitoes than the proposed 3-1-methyl-butanol lure.

Complex epidemiology and zoonotic potential for Cryptosporidium suis in rural Madagascar

Cryptosporidium spp. is the most important parasitic diarrheal agent in the world, is among the top four causes of moderate-to-severe diarrheal disease in young children in developing nations, and is problematic as an opportunistic co-infection with HIV. In addition, Cryptosporidium is a persistent challenge for livestock production. Despite its zoonotic potential, few studies have examined the ecology and epidemiology of this pathogen in rural systems characterized by high rates of overlap among humans, domesticated animals, and wildlife. To improve our understanding of the zoonotic potential of Cryptosporidium species in the rural tropics, we screened humans, livestock, peridomestic rodents, and wildlife using PCR-RFLP and sequencing-based approaches to distinguish species of Cryptosporidium in rural southeastern Madagascar. Cryptosporidium of multiple species/genotypes were apparent in this study system. Interestingly, C. suis was the dominant species of Cryptosporidium in the region, infecting humans (n=1), cattle (n=18), pigs (n=3), and rodents (n=1). The broad species range of C. suis and the lack of common cattle Cryptosporidium species (Cryptosporidium parvum and Cryptosporidium andersoni) in this system are unique. This report represents the fifth confirmed case of C. suis infection in humans, and the first case in Africa. Few rural human and livestock populations have been screened for Cryptosporidium using genus-specific genotyping methods. Consequently, C. suis may be more widespread in human and cattle populations than previously believed.

Teeth, sex, and testosterone: aging in the world's smallest primate

Mouse lemurs (Microcebus spp.) are an exciting new primate model for understanding human aging and disease. In captivity, Microcebus murinus develops human-like ailments of old age after five years (e.g., neurodegeneration analogous to Alzheimer's disease) but can live beyond 12 years. It is believed that wild Microcebus follow a similar pattern of senescence observed in captive animals, but that predation limits their lifespan to four years, thus preventing observance of these diseases in the wild. Testing whether this assumption is true is informative about both Microcebus natural history and environmental influences on senescence, leading to interpretation of findings for models of human aging. Additionally, the study of Microcebus longevity provides an opportunity to better understand mechanisms of sex-biased longevity. Longevity is often shorter in males of species with high male-male competition, such as Microcebus, but mouse lemurs are sexually monomorphic, suggesting similar lifespans. We collected individual-based observations of wild brown mouse lemurs (Microcebus rufus) from 2003-2010 to investigate sex-differences in survival and longevity. Fecal testosterone was measured as a potential mechanism of sex-based differences in survival. We used a combination of high-resolution tooth wear techniques, mark-recapture, and hormone enzyme immunoassays. We found no dental or physical signs of senescence in M. rufus as old as eight years (N = 189, ages 1-8, mean = 2.59 ± 1.63 SE), three years older than captive, senescent congeners (M. murinus). Unlike other polygynandrous vertebrates, we found no sex difference in age-dependent survival, nor sex or age differences in testosterone levels. While elevated male testosterone levels have been implicated in shorter lifespans in several species, this is one of the first studies to show equivalent testosterone levels accompanying equivalent lifespans. Future research on captive aged individuals can determine if senescence is partially a condition of their captive environment, and studies controlling for various environmental factors will further our understanding of senescence.

Pathogenic enterobacteria in lemurs associated with anthropogenic disturbance

As human population density continues to increase exponentially, speeding the reduction and fragmentation of primate habitat, greater human-primate contact is inevitable, making higher rates of pathogen transmission likely. Anthropogenic effects are particularly evident in Madagascar, where a diversity of endemic lemur species are threatened by rapid habitat loss. Despite these risks, knowledge of how anthropogenic activities affect lemur exposure to pathogens is limited. To improve our understanding of this interplay, we non-invasively examined six species of wild lemurs in Ranomafana National Park for enteric bacterial pathogens commonly associated with diarrheal disease in human populations in Madagascar. Patterns of infection with Enterotoxigenic Escherichia coli, Shigella spp., Salmonella enterica, Vibrio cholerae, and Yersinia spp. (enterocolitica and pseudotuberculosis) were compared between lemurs inhabiting intact forest and lemurs inhabiting degraded habitat with frequent exposure to tourism and other human activity. Fecal samples acquired from humans, livestock, and rodents living near the degraded habitat were also screened for these bacteria. Remarkably, only lemurs living in disturbed areas of the park tested positive for these pathogens. Moreover, all of these pathogens were present in the human, livestock, and/or rodent populations. These data suggest that lemurs residing in forests altered or frequented by people, livestock, or peridomestic rodents, are at risk for infection by these diarrhea-causing enterobacteria and other similarly transmitted pathogens.

Relatedness communicated in lemur scent

Lemurs are the most olfactory-oriented of primates, yet there is still only a basic level of understanding of what their scent marks communicate. We analyzed scent secretions from Milne-Edwards' sifakas (Propithecus edwardsi) collected in their natural habitat of Ranomafana National Park, Madagascar. We sought to test whether the scent mark could signal genetic relatedness in addition to species, sex, season, and individuality. We not only found correlations (r (2) = 0.38, P = 0.017) between the total olfactory fingerprint and genetic relatedness but also between relatedness and specific components of the odor, despite the complex environmental signals from differences in diet and behavior in a natural setting. To the best of our knowledge, this is the first demonstration of an association between genetic relatedness and chemical communication in a wild primate population. Furthermore, we found a variety of compounds that were specific to each sex and each sampling period. This research shows that scent marks could act as a remote signal to avoid inbreeding, optimize mating opportunities, and potentially aid kin selection.

Change of carbon source causes dramatic effects in the phospho-proteome of the archaeon Sulfolobus solfataricus

Protein phosphorylation is known to occur in Archaea. However, knowledge of phosphorylation in the third domain of life is rather scarce. Homology-based searches of archaeal genome sequences reveals the absence of two-component systems in crenarchaeal genomes but the presence of eukaryotic-like protein kinases and protein phosphatases. Here, the influence of the offered carbon source (glucose versus tryptone) on the phospho-proteome of Sulfolobus solfataricus P2 was studied by precursor acquisition independent from ion count (PAcIFIC). In comparison to previous phospho-proteome studies, a high number of phosphorylation sites (1318) located on 690 phospho-peptides from 540 unique phospho-proteins were detected, thus increasing the number of currently known archaeal phospho-proteins from 80 to 621. Furthermore, a 25.8/20.6/53.6 Ser/Thr/Tyr percentage ratio with an unexpectedly high predominance of tyrosine phosphorylation was detected. Phospho-proteins in most functional classes (21 out of 26 arCOGs) were identified, suggesting an important regulatory role in S. solfataricus. Focusing on the central carbohydrate metabolism in response to the offered carbon source, significant changes were observed. The observed complex phosphorylation pattern hints at an important physiological function of protein phosphorylation in control of the central carbohydrate metabolism, which might particularly operate in channeling carbon flux into the respective metabolic pathways.

Seasonal mortality patterns in non-human primates: implications for variation in selection pressures across environments

Examining seasonal mortality patterns can yield insights into the drivers of mortality and thus potential selection pressures acting on individuals in different environments. We compiled adult and juvenile mortality data from nine wild non-human primate taxa to investigate the role of seasonality in patterns of mortality and address the following questions: Is mortality highly seasonal across species? Does greater environmental seasonality lead to more seasonal mortality patterns? If mortality is seasonal, is it higher during wet seasons or during periods of food scarcity? and Do folivores show less seasonal mortality than frugivores? We found seasonal mortality patterns in five of nine taxa, and mortality was more often tied to wet seasons than food-scarce periods, a relationship that may be driven by disease. Controlling for phylogeny, we found a positive relationship between the degree of environmental seasonality and mortality, with folivores exhibiting more seasonal mortality than frugivores. These results suggest that mortality patterns are influenced both by diet and degree of environmental seasonality. Applied to a wider array of taxa, analyses of seasonal mortality patterns may aid understanding of life-history evolution and selection pressures acting across a broad spectrum of environments and spatial and temporal scales.

Aye-aye (Daubentonia madagascariensis) feeding strategies at Ranomafana National Park, Madagascar: an indirect sampling method

In this research, we focused on aye-aye populations in Ranomafana National Park, Madagascar. From August to December 2008, we tested how aye-aye feeding was influenced by presence/absence of both fruiting and non-fruiting Canarium trees. Deadwood feeding traces were used as a proxy for evidence of Canarium feeding. We enumerated deadwood feeding traces in 20 locations, 10 with Canarium, 10 without. Each location contained two transects (80 m L × 20 m W) for a total area of 5.6 ha. Feeding trace results for Canarium locations compared to non-Canarium locations were not significant (Z = -1.926, p = 0.083); however, feeding trace results were significant when comparing fruiting and non-fruiting Canarium locations (Z = -2.417, p = 0.016). These results highlight the importance of Canarium in the diet of aye-ayes and demonstrate how the distribution of this resource may influence the foraging behavior of aye-ayes.

Mapping the social network: tracking lice in a wild primate (Microcebus rufus) population to infer social contacts and vector potential

BACKGROUND

Studies of host-parasite interactions have the potential to provide insights into the ecology of both organisms involved. We monitored the movement of sucking lice (Lemurpediculus verruculosus), parasites that require direct host-host contact to be transferred, in their host population of wild mouse lemurs (Microcebus rufus). These lemurs live in the rainforests of Madagascar, are small (40 g), arboreal, nocturnal, solitary foraging primates for which data on population-wide interactions are difficult to obtain. We developed a simple, cost effective method exploiting the intimate relationship between louse and lemur, whereby individual lice were marked, without removal from their host, with an individualized code, and tracked throughout the lemur population. We then tested the hypotheses that 1) the frequency of louse transfers, and thus interactions, would decrease with increasing distance between paired individual lemurs; 2) due to host polygynandry, social interactions and hence louse transfers would increase during the onset of the breeding season; and 3) individual mouse lemurs would vary in their contributions to the spread of lice.

RESULTS

We show that louse transfers involved 43.75% of the studied lemur population, exclusively males. Louse transfers peaked during the breeding season, perhaps due to increased social interactions between lemurs. Although trap-based individual lemur ranging patterns are restricted, louse transfer rate does not correlate with the distance between lemur trapping locales, indicating wider host ranging behavior and a greater risk of rapid population-wide pathogen transmission than predicted by standard trapping data alone. Furthermore, relatively few lemur individuals contributed disproportionately to the rapid spread of lice throughout the population.

CONCLUSIONS

Using a simple method, we were able to visualize exchanges of lice in a population of cryptic wild primates. This method not only provided insight into the previously unseen parasite movement between lemurs, but also allowed us to infer social interactions between them. As lice are known pathogen vectors, our method also allowed us to identify the lemurs most likely to facilitate louse-mediated epidemics. Our approach demonstrates the potential to uncover otherwise inaccessible parasite-host, and host social interaction data in any trappable species parasitized by sucking lice.