African bushpigs exhibit porous species boundaries and appeared in Madagascar concurrently with human arrival

Several African mammals exhibit a phylogeographic pattern where closely related taxa are split between West/Central and East/Southern Africa, but their evolutionary relationships and histories remain controversial. Bushpigs (Potamochoerus larvatus) and red river hogs (P. porcus) are recognised as separate species due to morphological distinctions, a perceived lack of interbreeding at contact, and putatively old divergence times, but historically, they were considered conspecific. Moreover, the presence of Malagasy bushpigs as the sole large terrestrial mammal shared with the African mainland raises intriguing questions about its origin and arrival in Madagascar. Analyses of 67 whole genomes revealed a genetic continuum between the two species, with putative signatures of historical gene flow, variable FST values, and a recent divergence time (<500,000 years). Thus, our study challenges key arguments for splitting Potamochoerus into two species and suggests their speciation might be incomplete. Our findings also indicate that Malagasy bushpigs diverged from southern African populations and underwent a limited bottleneck 1000-5000 years ago, concurrent with human arrival in Madagascar. These results shed light on the evolutionary history of an iconic and widespread African mammal and provide insight into the longstanding biogeographic puzzle surrounding the bushpig's presence in Madagascar.

Bushpig (Potamochoerus larvatus) Hunting in Rural Areas of Madagascar and Its Health and Socioeconomic Implications

Bushmeat consumption and trade plays a relevant role in many tropical countries as a source of protein and income for rural populations. In Madagascar, rural populations depend heavily on natural resources and wildlife as source of income and protein. The bushpig (Potamochoerus larvatus) is the largest mammal available in the island and regularly hunted. However, little is known about the importance and characteristics of this activity and its implication as a potential source of pathogens for both humans and domestic animals. A cross-sectional study was conducted in 2014–2015 in five different regions of rural Madagascar suspected to have significant bushpig populations to (i) quantify and characterize the importance of bushpig hunting, (ii) assess the socioeconomic impact of bushpig trade, (iii) evaluate the potential pathogen transmission between bushpigs, domestic pigs and humans. A total of 77 hunters, 10 butchers and 95 pig farmers were individually interviewed. Hunting seasonality and the perception of local hunters with regards to the dynamics of bushpig populations in the last decade differed between the tropical dry and tropical sub-arid climatic zones. The top reason for hunting bushpigs was crop protection but personal consumption and selling of meat were also common. Hunting efficacy was largely dependent on the technique used. Snares and traps, the most widely used techniques, allowed the majority of hunters to catch from one to 10 bushpigs per year. Limited commercial bushpig trade was observed with only 0.8 bushpig sold in average per year and per hunter, representing a 16 USD income. The average price per kilo sold was USD 0.8 and the average profit received by each butcher/collector after the sale of a carcass was USD 11.9. No perception of disease risks nor precautions were taken to prevent potential pathogen transmission from bushpig to humans or pigs. Most of the hunters (68%) indicated that they had never seen a diseased bushpig. Bushpig hunting in our study areas in Madagascar was basically a small-scale subsistence hunting, very different from commercial bushmeat hunting described in areas of Central Africa or the Amazon Basin. More research is needed to verify the sustainability of bushpig hunting and its potential role in terms of reducing pressure on other endemic wildlife species and transmitting pathogens to humans and pigs.

Genetic origins and diversity of bushpigs from Madagascar (Potamochoerus larvatus, family Suidae)

The island of Madagascar, situated off the southeast coast of Africa, shows the first evidence of human presence ~ 10,000 years ago; however, other archaeological data indicates a settlement of the modern peoples of the island distinctly more recent, perhaps > 1500 years ago. Bushpigs of the genus Potamochoerus (family Suidae), are today widely distributed in Madagascar and presumed to have been introduced from Africa at some stage by human immigrants to the island. However, disparities about their origins in Madagascar have been presented in the literature, including the possibility of endemic subspecies, and few empirical data are available. Furthermore, the separation of bushpigs in Madagascar from their mainland relatives may have favoured the evolution of a different repertoire of immune genes first due to a founder effect and then as a response to distinct pathogens compared to their ancestors. Molecular analysis confirmed the species status of the bushpig in Madagascar as P. larvatus, likely introduced from the central region of southern Africa, with no genetic evidence for the recognition of eastern and western subspecies as suggested from previous cranial morphology examination. Investigation of the immunologically important SLA-DQB1 peptide-binding region showed a different immune repertoire of bushpigs in Madagascar compared to those on the African mainland, with seventeen exon-2 haplotypes unique to bushpigs in Madagascar (2/28 haplotypes shared). This suggests that the MHC diversity of the Madagascar populations may have enabled Malagasy bushpigs to adapt to new environments.

Serological Evidence of West Nile and Usutu Viruses Circulation in Domestic and Wild Birds in Wetlands of Mali and Madagascar in 2008

The geographical distribution and impact on animal and human health of both West Nile and Usutu viruses, two flaviviruses of the Japanese encephalitis complex, have been increasing during the past two decades. Both viruses circulate in Europe and Africa within a natural cycle between wild birds and mosquitoes, mainly from the Culex genus. We retrospectively analyzed sera from domestic and wild birds sampled in 2008 in two wetlands, namely the Inner Niger Delta, Mali, and the Lake Alaotra area, Madagascar. Sera were first tested using a commercial ID Screen West Nile Competition Multi-species ELISA kit. Then, positive sera and sera with insufficient volume for testing with ELISA were tested with a Microneutralization Test. In Mali, the observed seroprevalence in domestic birds was 28.5% [24.5; 32.8] _95%CI, 3.1 % [1.8; 5.2] _95%CI, 6.2% [3.4; 10.2] _95%CI and 9.8 % [7.3; 12.8] _95%CI, for West Nile virus (WNV), Usutu virus (USUV), undetermined flavivirus, and WNV/USUV respectively. Regarding domestic birds of Madagascar, the observed seroprevalence was 4.4 % [2.1; 7.9]_95%CI for WNV, 0.9% [0.1; 3.1] _95%CI for USUV, 1.3% [0.5; 2.8] _95%CI for undetermined flavivirus, and null for WNV/USUV. Among the 150 wild birds sampled in Madagascar, two fulvous whistling-ducks (Dendrocygna bicolor) were positive for WNV and two for an undetermined flavivirus. One white-faced whistling-duck (Dendrocygna viduata) and one Hottentot teal (Spatula hottentota) were tested positive for USUV. African and European wetlands are linked by wild bird migrations. This first detection of USUV—as well as the confirmed circulation of WNV in domestic birds of two wetlands of Mali and Madagascar—emphasizes the need to improve the surveillance, knowledge of epidemiological patterns, and phylogenetic characteristics of flavivirus in Africa, particularly in areas prone to sustained, intense flavivirus transmission such as wetlands.

Shotgun sequencing of the mitochondrial genome of the Aldabra giant tortoise (Aldabrachelys gigantea)

The complete mitochondrial genome of the Aldabra giant tortoise [Aldabrachelys gigantea (Schweigger, 1812): Reptilia, Testudines, Testudinidae] was sequenced using a shotgun approach on an Illumina HiSeq 2500 platform (Illumina Inc., San Diego, CA). This genome was 16 467 bp long and presents the typical organization found in vertebrates. The mean coverage of sequencing was 116×. A phylogenetic analysis of the Testudinidae confirms the placement of Aldabrachelys in an Indian Ocean group (including Madagascar). This mitogenome constitutes a reference for ancient DNA analyses of the extinct Madagascan lineages of Aldabrachelys.

How to reach the poor? Surveillance in low-income countries, lessons from experiences in Cambodia and Madagascar

Surveillance of animal diseases in developing countries faces many constraints. Innovative tools and methods to enhance surveillance in remote and neglected areas should be defined, assessed and applied in close connection with local farmers, national stakeholders and international agencies. The authors performed a narrative synthesis of their own publications about surveillance in Madagascar and Cambodia. They analysed the data in light of their fieldwork experiences in the two countries' very challenging environments. The burden of animal and zoonotic diseases (e.g. avian influenza, African swine fever, Newcastle disease, Rift Valley fever) is huge in both countries which are among the poorest in the world. Being poor countries implies a lack of human and financial means to ensure effective surveillance of emerging and endemic diseases. Several recent projects have shown that new approaches can be proposed and tested in the field. Several advanced participatory approaches are promising and could be part of an innovative method for improving the dialogue among different actors in a surveillance system. Thus, participatory modelling, developed for natural resources management involving local stakeholders, could be applied to health management, including surveillance. Data transmission could benefit from the large mobile-phone coverage in these countries. Ecological studies and advances in the field of livestock surveillance should guide methods for enhancing wildlife monitoring and surveillance. Under the umbrella of the One Health paradigm, and in the framework of a risk-based surveillance concept, a combination of participatory methods and modern technologies could help to overcome the constraints present in low-income countries. These unconventional approaches should be merged in order to optimise surveillance of emerging and endemic diseases in challenging environments.

Abondance du potamochère, Potamochoerus larvatus, dans les savanes du Nord-Ouest de Madagascar et risques épidémiologiques associés

Le potamochère, Potamochoerus larva- tus, est un réservoir sauvage potentiel de maladies enzootiques à Madagascar. Parmi celles-ci, la peste porcine africaine (Ppa) est une des plus inquiétantes. Diag- nostiquée dans ce pays depuis 1998, cette maladie virale majeure d’un point de vue socio-économique est inféodée aux suidés et y est encore aujourd’hui très répandue. La caractérisation des voies de transmission du virus entre pota- mochères et porcs domestiques est une étape préliminaire indispensable à la mise en œuvre d’une prophylaxie sani- taire contre la Ppa. Cette étude a pour objectif de préciser le risque de transmis- sion de la maladie entre potamochères et porcs domestiques dans les savanes périphériques du Parc national de l’Anka- rafantsika, dans le Nord-Ouest de Mada- gascar, où sont présents de nombreux élevages porcins. La méthode des Indices kilométriques d’abondance a permis de mettre en évidence une augmentation significative de l’abondance de ces sui- dés sauvages hors de la forêt durant la période de fructification de Strychnos spi- nosa. Le risque de transmission de la Ppa durant cette période apparaît donc plus élevé dans les sites où sont présents ces arbustes. Sur le plan épidémiologique, la maturité et l’occupation spatiale de S. spinosa peuvent servir d’indicateurs de présence du potamochère dans l’ouest de Madagascar. Son utilisation pour adapter les pratiques d’élevage dans une optique de réduction des contacts pourrait limiter le risque de contamination potentielle par le virus de la Ppa ou d’autres agents pathogènes transmis par les suidés sauvages. 

Isolation and characterization of six polymorphic microsatellite loci for the Malagasy spider tortoise, Pyxis arachnoides and cross-amplification in Pyxis planicauda

Pyxis arachnoides is a Critically Endangered Malagasy tortoise for which little data about its natural history and genetic variation are available. This lack of knowledge complicates undertaking conservation measures considering Pyxis genetic diversity. Here, we describe six new microsatellites for Pyxis arachnoides from wild specimens and several localities, and the cross amplification of two Astrochelys radiata microsatellites. Of these microsatellites, two are monomorphic among the three distinct subspecies and a closely related species, while the remaining six are polymorphic. Microsatellite data are needed for this species to study the inter- and intra-subspecies genetic diversity, especially for the highly endangered subspecies P. a. brygooi, which currently occurs only in remote localities. The availability of polymorphic microsatellites will allow identifying the population of origin of individuals and will aid in justifying their management as separate evolutionary lineages for conservation purposes. The rationale is to preserve both evolutionary processes and adaptive potential.

Local extinction in the bird assemblage in the greater Beijing area from 1877 to 2006

Recent growth in industrialization and the modernization of agricultural activities, combined with human population growth, has greatly modified China's natural environment, particularly in the vicinity of large cities. We compared avifauna checklists made between 1877 and 1938 with current checklists to determine the extent of local bird extinctions during the last century in the greater Beijing area. Our study shows that of the 411 bird species recorded from 1877-1938, 45 (10.9%) were no longer recorded from 2004-2006. Birds recorded as 'rare' in 1938 were more likely to have disappeared in subsequent years. Migrant status also influenced the probability of local bird extinction with winter migrants being the most affected class. Moreover, larger birds were more likely to have disappeared than smaller ones, potentially explained by differential ecological requirements and anthropogenic exploitation. Although our habitat descriptions and diet classification were not predictors of local bird extinction, the ecological processes driving local bird extinction are discussed in the light of historical changes that have impacted this region since the end of the 1930 s. Our results are of importance to the broader conservation of bird wildlife.