Biology subjects

Meijaard, E.

Publications and source records attributed to Meijaard, E..

11 recordsLinked to original sources

bioRxiv2025

From deserts to forests: sequencing of the giant forest hog completes the genomic history of the African Suids

The giant forest hog (GFH, Hylochoerus meinertzhageni), the largest and most elusive wild pig, is found in a disjunct range across equatorial Africa, primarily inhabiting forests and woodlands. It is the only remaining African suid species without whole-genome data. The GFH is currently classified into three subspecies, differing in skull morphology and size. Here, we present the first whole-genome data of nine GFHs; one from Guinea and eight Uganda, representing the two geographically most distant subspecies. This genomic evidence allowed us to resolve the previously uncertain placement of the GFH among African suids as a sister group to the warthogs (Phacochoerus spp.). Also, we found a deep evolutionary split between the two GFH populations resulting in a level of genetic differentiation (FST > 0.75), which is similar to or higher than values observed among species of African wild pigs. The GFH likely diverged from warthogs around 4.6 Mya while the two study populations of GFH diverged at least 0.5 Mya and, subsequently, experienced very dissimilar demographic trajectories. The individual from Guinea had half of the heterozygosity level of the Uganda population, and lower value compared to all the African suids, probably as a result of the long term low Ne and isolation. Due to the close affinity of GFH with the African rainforest biotic zone, our findings have implications for understanding the history of habitat change in Africa. They also indicate a very deep and previously underappreciated evolutionary divergence within the GFH that may have implications for its conservation.

genomics↗

bioRxiv2025

Occupancy estimation of wild species in a palm oil plantation using unstructured data

In 2020-2024, plantation workers at a large oil palm plantation in West Kalimantan recorded sightings of wild species of several species groups. They did not use a standardized field method and produced no comprehensive reports but recorded only one or a few species per visit. Such unstructured data are generally viewed as challenging for statistical analysis. Here, we used occupancy models to estimate what proportion of spatial units (both non-natural and forest) a given species occupied annually in the plantation. We tested models with different covariates for species for which most data were available: 13 birds, 3 reptiles and 7 mammals, among which the iconic Orangutan (Pongo pygmaeus). For each species, the model which best fitted the data was selected. Two shortcomings in our data complicated the analyses. First, occupancy models require detection and non-detection records, but because no fixed species lists were used, there is no unique way to generate non-detections. We generated non-detection records in several ways and ran the models again to evaluate the consequences for occupancy estimates. Second, imbalances in sampling may occur because of a lack of sampling design to select study sites. Most concerning are sites surveyed only once in 2020-2024. We ran the models without those sites to examine whether results were different. Although the shortcomings mentioned turned out not to distort our results, the occupancy estimates were imprecise for many study species because of low detection rates, and extra efforts are needed to improve that.

bioinformatics↗

bioRxiv2025

Genomic and morphometric evidence for Austronesian-mediated pig translocation in the Pacific

Human mediated translocation of non-native pig species (genus Sus) to the islands of Wallacea and Oceania has significantly altered local ecosystems. To investigate the timing and trajectory of these introductions, we conducted both genomic analyses of 576 pig nuclear genomes and a geometric morphometric analysis of 714 modern and ancient dental remains. Our analyses demonstrate that feral and domestic pigs in Wallacea and Oceania possess diverse ancestries resulting from the introduction of multiple, sequential pig populations followed by gene flow. Despite the variability in their genomic ancestry these pigs all possess a distinct tooth morphology, and a genetic link to the Chinese domestic pig populations that accompanied the dispersal of Austronesian language speakers [~]4,000-3,000 years ago via Taiwan and the Philippines.

evolutionary biology↗

bioRxiv2025

A novel citizen science-based wildlife monitoring and management tool for oil palm plantations

Agricultural expansion is one of the greatest threats to global biodiversity. At the same time, many wildlife species survive or even thrive in agricultural landscapes that retain patches of natural ecosystems. This is especially true for tropical oil palm (Elaeis guineensis, Jacq.) plantations that have both replaced tropical forest and other species-rich ecosystems, but as perennial crops can also function as wildlife habitat, especially if fragments of natural ecosystems are retained. There is an urgent need to understand how to manage and monitor wildlife in these fragmented oil palm landscapes. Still, the lack of large, quantitative datasets on species abundance impedes learning. We piloted a novel citizen science-based biodiversity monitoring system in Austindo Nusantara Jayas seven Indonesian oil palm estates, across different biogeographical regions, over a 5-year period. The company-wide monitoring system called PENDAKI, the Indonesian acronym for Care for Biodiversity, is the first of its kind in the palm oil industry. Here we demonstrate that such unstructured and opportunistic data collected mainly by lay people can result in valuable information on temporal and spatial changes in species occupancy. Between September 2019 and June 2024, PENDAKI has resulted in 148,286 wildlife observations, that included 699 reliably identified faunal and 186 floral species, with contributions from 3,950 employee contributors. We estimate species-specific occupancy rates using Bayesian occupancy modeling, ideally suited for opportunistic data where survey effort is unknown. We show that these occupancy data can reliably show temporal and spatial changes in the distribution of iconic wildlife such as orangutans (Pongo pygmaeus). We combined data from reliably identified species with at least 50 records to create the "Living Plantation Index", an estate-specific annual index of wildlife diversity based on occupancy estimates. We conclude that citizen science-based biodiversity monitoring works remarkably well in oil palm plantations because of the large number of people typically working there. In the process we discovered the emergence of co-benefits such as increasing environmental stewardship awareness across the workforce, raising the profile of the conservation department within the company. We also noted the benefits in terms of suitable data to meet regulatory and voluntary disclosure requirements.

scientific communication and education↗

bioRxiv2021

Deforestation projections imply range-wide population decline for critically endangered Bornean orangutan

Assessing where wildlife populations are at risk from future habitat loss is particularly important for land-use planning and avoiding biodiversity declines. Combining projections of future deforestation with species density information provides an improved way to anticipate such declines. Using the endemic and critically endangered Bornean orangutan (Pongo pygmaeus) as a case study we applied a spatio-temporally explicit deforestation model to forest loss data from 2001-2017 and projected future impacts on orangutans to the 2030s. Our projections point to continued deforestation across the island, amounting to a loss of forest habitat for 26,200 (CI: 19,500-34,000) orangutans. Populations currently persisting in forests gazetted for industrial timber and oil palm concessions, or unprotected forests outside of concessions, were projected to experience the worst losses within the next 15 years, amounting to 15,400 (CI: 12,000-20,500) individuals. Lowland forests with high orangutan densities in West and Central Kalimantan were also projected to be at high risk from deforestation, irrespective of land-use. In contrast, most protected areas and logging concessions currently harboring orangutans will continue to face low levels of deforestation. Our business-as-usual projections indicate the importance of protected areas, efforts to prevent the conversion of logged forests for the survival of highly vulnerable wildlife, and protecting orangutan habitat in plantation landscapes. The modeling framework could be expanded to other species with available density or occurrence data. Our findings highlight that species conservation should not only attempt to act on the current situation, but also be adapt to changes in drivers to be effective.

ecology↗

bioRxiv2021

Forest loss in Indonesian New Guinea: trends, drivers, and outlook

The rich forests of Indonesian New Guinea are threatened. We used satellite data to examine annual forest loss, road development and plantation expansion from 2001 to 2019, then developed a model to predict future deforestation in this understudied region. In 2019, 34.29 million hectares (Mha), or 83% of Indonesian New Guinea, supported old-growth forest. Over nineteen years, two percent (0.75 Mha) were cleared: 45% (0.34 Mha) converted to industrial plantations, roads, mine tailings, or other uses near cities; 55% (0.41 Mha) cleared by transient processes including selective natural timber extraction, inland water bodies-related processes, fires, and shifting agriculture. Industrial plantations expanded by 0.23 Mha, with the majority (0.21 Mha; 28% of forest loss) replacing forests and reaching 0.28 Mha in 2019 (97% oil palm; 3% pulpwood). The Trans-Papua Highway, a ~4,000 km national investment project, increased by 1,554 km. Positive correlations between highway and plantations expansion indicate these are linked processes. Plantations and roads grew rapidly after 2011, peaked in 2015/16, and declined thereafter. Indonesian government allocated 2.62 Mha of land for the development of industrial plantations (90% oil palm 10% pulpwood) of which 74% (1.95 Mha) remained forest in 2019. A spatial model predicts that an additional 4.5 Mha of forest could be cleared by 2036 if Indonesian New Guinea follows similar relationships to Indonesian Borneo. We highlight the opportunities for policy reform and the importance of working with indigenous communities, local leaders, and provincial government to protect the biological and cultural richness still embodied in this remarkable region.

ecology↗

bioRxiv2020

How widespread was the Tapanuli orangutan and what led to its decline?

The Tapanuli Orangutan (Pongo tapanuliensis) is the most threatened great ape species in the world. It is restricted to an area of about 1,000 km2 of upland forest where fewer than 800 animals survive in three declining subpopulations. Through a historical ecology approach involving analysis of newspaper, journals, books and museum records from the early 1800s to 2009, we demonstrate that historically Pongo tapanuliensis inhabited a much larger area, and across a much wider range of habitat types than now. Its current Extent of Occurrence is between 2.5% and 5.0% of the historical range in the 1890s and 1940s respectively. A combination of historical fragmentation of forest habitats, mostly for small-scale agriculture, and unsustainable hunting likely drove various populations to the south, east and west of the current population to extinction. This happened prior to the industrial-scale forest conversion that started in the 1970s. Our findings indicate how sensitive P. tapanuliensis is to the combined effects of habitat fragmentation and unsustainable take-off rates. Saving this species will require prevention of any further fragmentation and killings or other removal of animals from the remaining population. Without concerted action to achieve this, the remaining populations of P. tapanuliensis are doomed to become extinct within several orangutan generations.

zoology↗

bioRxiv2020

Extreme ecological specialization in a rainforest mammal, the Bornean tufted ground squirrel, Rheithrosciurus macrotis

The endemic Bornean tufted ground squirrel, Rheithrosciurus macrotis, has attracted great interest among biologists and the public recently. Nevertheless, we lack information on the most basic aspects of its biology. Here we present the first empirical data on the feeding ecology of tufted ground squirrels, and use data from 81 sympatric mammalian and avian vertebrates to place it within a broad comparative context. R. macrotis is a dedicated seed predator and shows much more extreme ecological specialization than any other vertebrate, feeding on a far smaller subset of available plant foods and demonstrating a greater reliance on a single plant species- Canarium decumanum-than any other vertebrate taxon. Our results suggest that R. macrotis plays an important, previously unknown role in the ecology of Bornean lowland forests, and highlight how much we have yet to learn about the fauna inhabiting some of the most diverse, and most severely threatened, ecosystems on the planet.

ecology↗

bioRxiv2020

The importance of orangutans in small fragments for maintaining metapopulation dynamics

Orangutans (Pongo spp.) occur at low densities and therefore large areas are necessary to sustain viable metapopulations, defined here as sets of conspecific units of individuals linked by dispersal. Historically, orangutans lived in large contiguous areas of intact rainforest, but are now increasingly found in agricultural and other landscapes modified by people. Here we collate evidence of orangutans utilizing isolated forest fragments (< 500 ha) within multiple-use landscapes dominated by oil palm monoculture across Borneo. Orangutan signs (i.e. nests) were evident in 76 fragments surveyed by helicopter, and in 50 of 70 additional fragments surveyed on the ground; on average 63 ha in size. This includes presence of adult resident females with dependent young confirmed in 40% of the fragments assessed by ground survey. Our study revealed some resident females are raising offspring in isolated forest patches within mature oil palm stands. This not only confirms that some forest patches can sustain orangutans, but indicates migratory males are capable of reaching these fragments scattered throughout the multiple-use landscape. Therefore, orangutans that use or live in even small isolated forest patches are an essential part of the overall metapopulation by maintaining gene flow between, and genetic connectivity within, populations distributed across larger multiple-use landscapes. Orangutan survival is commonly thought to be low in small, isolated forest patches, and the customary management strategy is to remove (translocate) these individuals and release them in larger forests. In some cases, translocations may be necessary, i.e. in case of fire or when the animals are in eminent danger of being killed and have no other refuge. However, the small amount of data available indicates that mortality rates during and after translocations are high, while the impacts of removing animals from spatially dispersed metapopulations are unknown. Therefore, we argue the current policy of routine translocation rather than conserving the species within human-modified landscapes could inadvertently decrease critical metapopulation functionality necessary for long-term viability. It is clear that orangutans need natural forest to survive, but our findings show that fragmented agricultural landscapes can also serve as complementary conservation areas in addition to fully protected areas if they are well designed with ecological connections, and if orangutan killing can be prevented. To achieve this, we call for a paradigm shift from the traditional large single forest model to one that emphasizes metapopulation functionality in the fragmented forest - human use matrix characteristic of the Anthropocene. Version 2 (20 May 2020): this manuscript is a non-peer reviewed preprint shared via the BiorXiv server while being considered for publication in a peer-reviewed academic journal. Please refer to the permanent digital object identifier (https://doi.org/10.1101/2020.05.17.100842). Under the Creative Commons license (CC-BY Attribution-Non Commercial-No Derivatives 4.0 International) you are free to share the material as long as the authors are credited, you link to the license, and indicate if any changes have been made. You may not share the work in any way that suggests the licensor endorses you or your use. You cannot change the work in any way or use it commercially.

ecology↗

bioRxiv2020

How many bird and mammal extinctions has recent conservation action prevented?

Aichi Target 12 of the Convention on Biological Diversity (CBD) aims to prevent extinctions of known threatened species. To measure its success, we used a Delphi expert elicitation method to estimate the number of bird and mammal species whose extinctions were prevented by conservation action in 1993 - 2020 (the lifetime of the CBD) and 2010 - 2020 (the timing of Aichi Target 12). We found that conservation prevented 21-32 bird and 7-16 mammal extinctions since 1993, and 9-18 bird and 2-7 mammal extinctions since 2010. Many remain highly threatened, and may still become extinct in the near future. Nonetheless, given that ten bird and five mammal species did go extinct (or are strongly suspected to) since 1993, extinction rates would have been 2.9-4.2 times greater without conservation action. While policy commitments have fostered significant conservation achievements, future biodiversity action needs to be scaled up to avert additional extinctions.

ecology↗

bioRxiv2019

The power of mixed survey methodologies for detecting decline of the Bornean orangutan

For many threatened species, it is difficult to assess precisely for large areas the change in their abundances over time and the relative impacts of climate and anthropogenic land use. This is because surveys of such species are typically restricted to small geographic areas, are conducted during short time periods, and use different survey protocols. We assessed the change in the abundance of Bornean orangutan Pongo pygmaeus morio in Sabah, Malaysia, and to identify environmental drivers affecting the change by integrating different types of survey data. We used nest count data obtained from aerial and ground transect surveys and occurrence data obtained from reconnaissance walks and interview survey over the past decade. We built a spatially-explicit dynamic population model within the Bayesian framework allowing these varying survey data to be analyzed jointly by explicitly accounting for each surveys sampling rate. We found that sampling rates vary across survey types, reflecting each surveys associated effort. Orangutan survival rates were strongly determined by natural forest extent and moderately by temperature. Orangutan migration rates across more than 1 km distance between forest patches were low, which underlines the importance of maintaining ecological connectivity. The paucity of species abundance data collected in a consistent manner over many years across broad extents often hinders the assessment of species population trend and their persistence across regional scales. We demonstrate that this can be addressed by integrating multiple survey data across different localities, provided that sampling rate inherent to each survey is accounted for.

ecology↗