Ecology

Our research involved work with animal subjects (unionid mussels and Round Goby fishes) and was conducted following relevant regulations and standard procedures. The field collections were carried out under Pennsylvania Fish and Boat Commission permits (# 2018-01-0136 and 2019-01-0026). The experimental protocols were approved by Penn State University’s Institutional Animal Care and Use Committee (IACUC# 201646941 and 201646962). All new DNA sequencing data are made publicly available in GenBank (with accession numbers provided in Table 1) and a BioProject (# PRJNA813547) of the National Center for Biotechnology Information40.Propensity of Round Goby to consume unionid mussels in a controlled lab settingStream table setupWe conducted lab experiments to observe the potential predation of juvenile freshwater mussels by the Round Goby, following standard research protocols for work with animal subjects (IACUC# 201646962, Penn State University). We constructed four artificial stream tables in an aquatic laboratory, each measuring 3 × 2 m and featuring two run and two pool sections (each 0.63 × 0.56 × 0.46 m). Water flow was produced using eight Homsay 920 GPH submersible water pumps, which pumped water from a central reservoir tub into each table at the start of each run section. The water flow direction was clockwise for stream tables 1 and 3, and counterclockwise for stream tables 2 and 4. Water pumped into the stream tables exited via two drains located medially of each run section, where it flowed back to the central reservoir tub. Each stream table was filled with a 6 mm layer of substrate consisting of a mixture of sand, gravel (4–6 mm), and crushed stone (size 2B, with an average size of ~ 19 mm). The day before each experiment, field technicians traveled to local streams and collected macroinvertebrates using one minute D-frame kick net samples for each of the four stream tables. The macroinvertebrates and associated substrate were transported back to the facility and were introduced into each stream table system.Preferential feeding experimentsBefore each experiment commenced, juvenile Plain Pocketbook mussels (Lampsillis cardium) were introduced into each stream table (with 165 mussel specimens for experiment 1 and 100 mussels for experiments 2 and 3). This  widespread and abundant species is not imperiled in Pennsylvania, and mussels were provided for this study by the White Sulphur Springs National Fish Hatchery located in southeast West Virgina. The mussels were allowed to acclimate in the stream tables for 2 h before commencing each experiment. Ten Round Gobies were introduced into each stream system (stream tables 1 and 2 for experiment 1, and all tables for experiments 2 and 3). The total length (from nose tip to caudal tip) of each fish was measured prior to introduction and after the termination of experiments 2 and 3. Experiment 1 was conducted for 3 weeks, while experiments 2 and 3 were conducted for 8 days. During these experiments, Round Gobies were allowed to exist in the systems and feed preferentially, on the mussels and macroinvertebrates, for the allotted time before each investigation concluded. We acknowledge that in these experiments, the mussel abundances are higher and macroinvertebrate densities lower and less rich than commonly occur in the natural stream environment. Further, the Round Goby fish densities used are much higher than currently in the French Creek watershed, though are comparable to what is currently seen in parts of the Great Lakes basin. Nonetheless, the experiment scenarios allowed us to observe if Round Gobies would consume the mussels when given the choice to feed on a variety of food items.Evaluation of unionids consumed by fishRound Gobies were removed from the stream tables upon completion of each experiment. They were euthanized using  > 250 mg/L buffered (pH ~ 7) tricaine-S (MS222) solution. The fish were submerged for 10 min beyond the cessation of opercular movement to ensure proper euthanasia, and tissues were collected after we confirmed complete euthanasia—compliant with AVMA guidelines and approved by the IACUC protocol. The Round Gobies were placed in a 10% solution of formalin for preservation, and after 2 weeks, they were rinsed with clean water and were placed in 70% ethanol for long-term storage. After fish were removed from the system, the water was drained, and the substrate was sifted to recover the remaining mussels. Mussels were counted, and live individuals were returned to holding tanks for use in subsequent experiments. To further assess whether Round Gobies had consumed mussels during the investigation, Round Gobies were x-rayed using a Bruker Skyscan 1176 micro-CT scanner. After that, the stomachs of each fish were excised, and the contents examined using a Leica CME dissection scope to confirm the identity of Plain Pocketbook mussels. Contents posterior to the stomach were not analyzed because they could not be reliably counted and identified.DNA metabarcoding to identify mussel species consumed by Round Goby in a stream settingFish and mussel sample acquisitionWe collected 39 Round Gobies directly from streams within the French Creek watershed—their newly invaded natural stream habitats—in June 2018. We aimed to quantify which species, if any, of unionid mussels they consumed. Fish collection locations included LeBoeuf Creek at Moore Road and 100 m below the confluence of French Creek and LeBoeuf Creek. The unionid mussel populations and the environmental field settings at these locations are detailed by Clark et al.19. A team of field technicians collected fish by kick seining (3 m × 1 m × 9.5 mm nylon mesh) while moving downstream. Seining was the sampling method of choice compared to electrofishing to avoid possible regurgitation of food items prior to excision of fishes’ stomachs. The stream reaches sampled at each location were between 100 and 200 m in length and included riffle, run, and pool habitats. In addition to fish samples, unionid mussel samples from French Creek were also collected for analysis (under Pennsylvania Fish & Boat Commission collectors permits # 2018-01-0136 and 2019-01-0026). Following standard research protocols (under IACUC# 201646941, Penn State University), the Round Gobies collected were euthanized using buffered Tricaine-S (MS222) solution; and stomachs were excised using sterilized utensils before being placed in sterilized tubes filled with 97% ethanol. After excision of stomachs, fishes were placed in a 10% formalin solution for preservation. After 2 weeks, fishes were rinsed with clean water and transferred to 70% ethanol for storage. The stomach samples were immediately placed in ethanol and on ice in the field. Samples were stored in a freezer before being shipped to the US Geological Survey’s Eastern Ecological Science Center for various molecular ecology analyses. Once the fish and mussel samples arrived at this lab, they were recorded and stored at four °C until analysis.Primer developmentSpecific primers targeting a moderately conserved region of the mitochondrial COI gene for 25 species of unionids inhabiting French Creek were designed. Previously a PCR-based amplification method utilizing restriction enzyme digests was used to identify genetic fingerprints of 25 unionid species inhabiting French Creek41. Here, we designed a new degenerate PCR primer set modified with sequencing overhangs to facilitate compatibility with a MiSeq amplicon sequencing method previously designed for 16S Amplicon sequencing. We targeted the locus of the mitochondrial COI gene of unionids known to inhabit the Atlantic Slope Drainage. Consensus sequences were derived using Multalin analysis and a tiling method to identify conserved primer binding regions flanking an ~ 300 bp region of the COI gene. This gene was targeted in part due to the availability of partial or complete sequences representing these target species in the NCBI reference database40. Cytochrome oxidase sequences were downloaded for the 25 unionid mussel species of interest. However, a COI sequence for the Rabbitsfoot (Theliderma cylindrica) mussel was absent from the NCBI database, which required us to sequence this region for an in-house reference (which is described later in the paper). We designed a degenerate primer cocktail specific to all mussel species of interest that amplified a ~ 289 bp product, with forward and reverse primers used for the amplification of unionid specific COI presented as supplemental information (see Table S-230. We evaluated the suitability of the primers using samples from field identified mussels. For primer optimization, PCR was run across a gradient of annealing temperatures to determine suitability. In addition, we used Round Goby DNA as a template to evaluate specificity. In addition to Round Goby stomach samples, mussel samples of several species collected from French Creek were included as positive controls.DNA extraction from tissue samplesFollowing the manufacturer’s protocols, tissue samples (including fish stomach and mussel tissue) were extracted with the Zymo Research ZymoBIOMICS 96 MagBead DNA Kit (San Diego, CA). Random samples of DNA extracts were analyzed on an Agilent 2100 Bioanalyzer using a high-sensitivity assay kit. Fragments in the target amplicon range were apparent (albeit not known to be of mussel origin). All samples were stored at − 20 °C until PCR was performed. DNA from both the T. cylindrica and L. complanata samples were analyzed for DNA quality.Rolling circle amplification of mitochondrial genomesTo acquire COI sequences for T. cylindrica and L. complanata, we subjected archived DNA samples to rolling circle amplification (RCA) followed by amplicon sequencing on the MiSeq. In short, 2 µl of DNA template was added to 2 µl Equiphi29 DNA polymerase reaction buffer containing 1 µl of Exonuclease-resistant random primers (ThermoFisher). Samples were denatured by heating to 95 °C for 3 min followed immediately by cooling on ice for more than 5 min. A volume of 5 µl was added to an RCA master mix containing 1.5 µl of 10 × Equiphi29 DNA polymerase reaction buffer, 0.2 µl of 100 mM dithiothreitol, 8 µl of 2.5 mM dNTPs, 1 µl of Eqiphi29 DNA polymerase (10U) and 4.3 µl of nuclease-free water. The samples were heated to 45 °C for 3 h and then 65 °C for 10 min. Samples were then placed in ice and then frozen at − 20 °C. All RCA products were normalized to 0.2 ng/µl in 10 mM Tris–HCl, pH 8.5. Normalized RCA product was utilized as a template for an Illumina Nextera XT library preparation. Sequencing libraries were prepared following the Nextera XT Library Preparation Reference Guide (CT# 15031942 v01) using the Nextera XT Library Preparation Kit (Illumina, San Diego, CA). Final libraries were analyzed for size and quality using the Agilent BioAnalyzer with the accompanying DNA 1000 Kit (Agilent, Santa Clara, CA). Libraries were quantified using the Qubit H.S. Assay Kit (Invitrogen, Carlsbad, CA) and normalized to 4 nM using 10 mM Tris, pH 8.5. Libraries were pooled and run on the Illumina MiSeq at a concentration of 10 pM with a 5% PhiX spike with run parameters of 1 × 150. Bioinformatic processing of this data is outlined below.Amplification of the cytochrome oxidase 1 geneExtracted genomic DNA was used as template for end-point PCR. Samples evaluated were from mussels and round gobies (see supporting Table S-330). The ~ 289 bp COI region was amplified with the mussel primers as follows. The amplification reaction contained 0.15 µM of each primer, 1 µL of the initial amplification product, and Promega Go Taq Green Master Mix following manufacturer recommendations for a 25 µL reaction. The thermocycler program consisted of an initial denaturing step of 95 °C for 3 min, followed by 30 cycles of 30 s at 95 °C, 30 s at 52 °C, and 1 min at 72 °C. Products were subjected to a final extension of 72 °C for 5 min then held until collection at 12 °C. An appropriately sized amplification product was confirmed for each reaction by electrophoresis of 5 µL of the reaction product through a 1.5% I.D. N.A. agarose gel (FMC Bioproducts) at 100 V for 45 min. PCR products were cleaned with the Qiagen Qiaquick PCR purification kit (Valencia, CA) and quantified using the Qubit dsDNA H.S. Assay Kit (Thermofisher Scientific, Grand Island, NY). Samples were diluted in 10 mM Tris buffer (pH 8.5) to a final concentration of 5 ng/µL.Generation of mock mussel samplesTo better understand and minimize sources of error or bias in the taxonomic assignment, we created a mock extraction by mixing sequences from known mussel taxa at defined concentrations. For each mussel, approximately 25-mg of tissue was extracted with the ZymoBIOMICS 96 MagBead DNA Kit (San Diego, CA) following the manufacturer’s protocol. The COI sequence was amplified from each species using the same primer-protocol combination described above. A total of 5 PCR products were mixed at equal concentration (mass/volume) to generate the mock sample (“Mock” hereafter). To confirm the identity of these inputs, each COI region was amplified and sequenced on the Illumina MiSeq during the same run as the Mock and samples.Sequencing library preparation and quality assessmentNext-generation sequencing was performed on the Illumina MiSeq platform to observe species-specific sequences and determine the diet of the Round Goby. Inclusion of the overhangs on the amplification primers allowed us to utilize the Illumina 16S Metagenomic Sequencing Library Preparation protocol42. Amplicon libraries were prepared following the same manufacturer’s protocol. All samples were indexed using the Illumina Nextera XT multiplex library indices. DNA read size spectra were determined with the Agilent 2100 Bioanalyzer using the Agilent DNA 1000 Kit (Santa Clara, Calif.). Libraries were quantified with the Qubit dsDNA H.S. Assay Kit (ThermoFisher Scientific, Grand Island, N.Y.) and normalized to 4 nM (nM) using 10 mM (mM) Tris (hydroxymethyl) aminomethane buffer pH 8.5. A final concentration of 10 picomolar library with a 6.5% PhiX control spike was created with the combined pool of all indexed libraries. All bioinformatic operations were completed on CLC Genomic Workbench v20 (Qiagen, Valencia, Calif.).Read filtering, trimming, and RNAseq metabarcoding assemblyFASTQ files from the sequencing runs were imported as paired-end reads into CLC Genomics Workbench v20.0.4 (Qiagen Bioinformatics, Redwood City, Calif.) for initial filtering of exogenous sequence adaptors and poor-quality base calls. The trimmed overlapping paired-end reads were mapped to the 25 target unionid sequences specific for the species of interest. Several mapping iterations were run using different levels of stringency. We utilized + 2/− 3 match-mismatch scoring and set the length fraction to 0.90. Analyses were iterated using different similarity fractions ranging from 0.90 to 0.99. Reads were annotated, and relative abundance was determined using a curated reference library (see supporting Datasets S-1 and S-230). More

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By pooling the results of the entire known range analysis of 14 GPS-collared elephants living in the Kinabatangan, our study suggests that this populations range covers at least 628 km2 (Table 3). Nine different locations were identified as hot spots, representing 266.9 km2 or 43% of this range, suggesting that just under half is highly used and/or frequented (Fig. 1). We found that the size of individual’s hot spots was positively related to the size of the entire range, meaning the larger the entire range the larger the summed area of an elephants hot spots. On average, hot spots represented a relatively small percent of an animal’s entire range (ranging from 4 to 20%, averaging 12%, Table 3). However, time spent within these hot spots ranged from 10 to 60% (averaging 34% across elephants, Table 5), with time spent in hot spots being related to the overall size of the hot spots (the larger the hot spot the more time elephants spent in them).Identifying the location of these hot spots is essential in designing appropriate management practices in collaboration with land users and identifying the best location for elephant corridors. In the last 25 years, forest cover in the Lower Kinabatangan has been drastically reduced and fragmented46, eroding the biodiversity value of this landscape. Today, this region has little remaining forests, and what is left is insufficient for sustaining the local elephant population10. Moreover, forests are highly fragmented along the Kinabatangan River, with a number of bottlenecks constraining elephant movements9. The situation in this landscape is getting worse because of further land clearances for agriculture, namely oil palm; as well as for the highly controversial Sukau Bridge and new road/highway that is planned for the region.Our analyses revealed a highly significant difference between the average proportions of protected area, unprotected forest, and oil palm estate extents within the elephant’s entire range; and a substantive, but not significant, difference across these land use/land cover types within hot spots (Table SI 4). At the individual level, there was a highly significant negative relationship between the proportion of protected areas and oil palm estates both within the elephant’s entire range and within the hot spots.At the pooled level, we found that around 45% of the entire known range and hot spots were within forested environments (280.44 km2 and 120.29 km2 respectively). Our results showed strong fidelity of certain elephants to these forested habitats. Our k-means cluster analysis found that within elephant entire ranges and hot spots, two out of the three cluster groups had high or very high usage of forests. Both cluster 1, for the entire range, and cluster 1 for hot spots extents, had five females that on average used forest environments 90% of their time, with protected areas being used 64% and 59%, and unprotected forested being used on average 26% and 31%, respectively (Table 7).Individuals in cluster 2, for the entire range analysis, on average, spent 73% of their time in forests (57% of this in protected areas and 16% in unprotected forests; Table 7). For the hot spot analysis, the individuals in cluster 2 spent on average 65% of their time in forests (52% of this in the unprotected forests and 13% in protected forests; Table 7). Elephants within these clusters were all females. Our results suggest that forest may be of particular importance for females as they had forest as their dominant land cover type within their entire range, hot spot extents and time spent analyses (Fig. 3, Table 5). Several studies have shown that adult females influence and guide the movement patterns and habitat utilization for their family group and that females in family units tend to inhabit less risky areas, such as within natural forest habitat60,61,62.However, the unprotected forest is at risk. We identified about 8% (or 49 km2) of forest identified within the pooled entire known range were not protected, with half potentially being on state land, and the remaining half on land titles of various types (Table SI 4). For the pooled hot spot areas, unprotected forest was proportionally higher, comprising of 11% (or 29 km2) of the total extent, with 54% being potentially on State land and 46% on land titles (Table SI 4). Protecting these forests would be an essential and efficient way to secure key elephant habitat since all collared individuals were using these forest fragments in their entire range (averaging 11%, and ranging from 8 to 18%), and hot spot extents (averaging 20%, and ranging from 0 to 53%) (Table SI 4, Fig. 3). On average, 24% of time was spent in unprotected forests within hot spots, though this varied widely from 0% (for the male elephant known as Gading) to 61% (for the female matriarch named Jasmine) (Table 5). In fact, five females had large proportions of their hot spot extents (24–53%) in unprotected forests, spending substantial periods of their time (33–61%) within these threatened areas.Our findings show that unprotected forests around the villages of Bilit and Sukau, were of particular significance (Figs. 1, 2). These unprotected forests largely consist of lowland dry forest, seasonally flooded swamp forest, and swamp forest, which are considered important habitats for elephants for feeding, resting and moving47,63. Within these forests, and along the forest margins and river banks there are also natural open grasslands that consist of Phragmites karka and Dinochloa scabrida that provide essential forage, mainly in the riparian areas for elephants9,21,23. Forested environments are also considered to be important in providing natural refugee from human activities and disturbance. For example, elephants have been documented to form significantly larger group sizes, as well as engaging in significantly more social interactions, in natural forest habitat compared to, for example, oil palm landscapes63. Adult females, generally, avoid areas considered unsafe for their respective social units, are more selective in the resources they use, and require regular access to water because of the presence of young64,65,66. This may be why our results, strongly suggest that forest habitats seem to be most important for adult females.Another significant issue faced by these elephants is the threat from the controversial planned Sukau bridge and road/highway that is set out in the Sabah Structure Plan, an overarching policy document for the State58. Currently, a new road/highway is under construction on the northern bank of the village of Sukau, and this has already cleared areas of unprotected forest. This public road could link to a potential new bridge that would cross over the Kinabatangan River, cutting through unprotected forest and a protected area (Lower Kinabatangan Wildlife Sanctuary), before going through oil palm estates then through another protected area to the south and through the Tabin elephant population range. For the Kinabatangan, creating a public highway will cut the elephant population range into two parts (Figs. 2, 3). All collared elephants use this area, as it is a key bottleneck and the only alternative option to pass around Sukau village9. We found that nine elephants have hot spots that intersect or meet up with the current road (which will be up-graded and get considerably busier) and/or the planned road/highway alignment (Figs. SI 1 and 2). For these elephants, we calculated that they spent from 2 to 44% (average 14%) of their time within these hot spots (Table 4). Our statistical analyses suggest that if the road/highway goes ahead it will have a significant impact on the elephants’ behaviour with respect to time spent in the hot spots. Indeed, this infrastructure project could have dire consequences for these elephants and their family groups, by disrupting their ranging patterns and segmenting the entire elephant range into two (Figs. 2, 4). The existing road in Batu Putih has already proven to be an impassable barrier for this elephant population, as no elephants have been observed crossing this road since the early 2000s14. For elephants that do try and cross, vehicle collisions may become a significant threat to elephants and drivers alike67, and potentially increasing human–elephant conflict in the nearby villages, as well as in plantations14,68,69, exacerbating an already difficult situation for this small and fragmented population.Results from the pooled analysis show that about 53% of the entire known population range is within oil palm estates; and 51% for the pooled hot spots (Fig. 3, Table SI 4). Our k-means clustering analysis grouped 6 elephants into cluster 3 that on average spent 57% of time in oil palm estates; and 7 elephants into cluster 2 within the hot spot analysis that on average spent 73% of their time in oil palm estates (Table 6). All the males, were clustered within these groups (Table 5). In fact, the three collared males were amongst the highest users of oil palm estates (Fig. 3, Table SI4, and 5). This could be related to a ‘‘high risk, high gain’’ strategy, often adopted by males to increase body size and enhance reproductive success32,33,60. However, it is interesting to see that three females (Ita, Ratu and Koyah) and their respective social units, also seemed to have high levels of oil palm use, while other individuals had zero or very little use of oil palm (e.g. Aqeela, Jasmin, Sandi, Kasih; Table SI 4, Fig. 3). Differential choices may result from differences in individual knowledge and experience with people during past encounters, for example70,71.We identified that collared elephants were ranging in 11 known oil palm estates, with the five most regularly used being Melangking Oil Palm Plantation (with 12 elephants entire range overlapping with this estate and six hot spots), IOI Corporation (with 11 overlapping entire ranges, and eight hot spots), Genting Plantations (14 and seven, respectively), Sime Darby Plantation (five and two, respectively), and Karangan Agriculture (8 and 2, respectively) (Table 6; Fig. 4). Presence of bottlenecks and barriers (e.g. electric fences) may explain hot spot occurrences in these estates, as well as feeding opportunities, management strategies of specific estates, and historical and seasonal ranges.Linear features like major highways, electric fences and drainage ditches hamper elephant movements within the Lower Kinabatangan9. A previous study identified 20 bottlenecks in the Lower Kinabatangan with the two main ones (of 9 km and 6.5 km in length) found around the village of Sukau9. In addition, the unplanned and chaotic erection of electric fences by large estates and smallholdings has disrupted significantly elephant movement patterns and resulted in artificial hot spots for certain individuals (e.g. Liun, Ita, Gading and Sejati)35,72. Electric fences have widely been used to mitigate human–elephant conflicts. The establishment of fences rarely consider the traditional elephant routes nor the location of existing fences in neighbouring estates. If elephants manage to enter such areas, they often become trapped and experience difficulties in returning to nearby forests, exacerbating conflicts with people35.Certain estates such as Melangking Oil Palm Plantation have allowed elephants to roam freely in their estate (Muhammad Al-Shafieq, personal communication). Since 2017, this plantation has shown a drastic reduction in damages to their oil palms following the removal of their permanent electric fences surrounding their entire estate. Instead, this plantation is using a temporary electric fencing regime around newly planted palm areas. Concurrently, they now do not push elephants out of their estate, which can explain why Melangking Oil Palm Plantation is a significant hotspot in the region.Another reason why elephant ranges incorporate oil palm estates is to move between forest patches that are becoming completely isolated following forest conversion, as is the case close to Sukau (Fig. SI1 and SI2; Fig. 1). Unlike other elephant species that increase their speed of movement rates in highly disturbed areas27,30,66, the Bornean elephant has been observed doing the opposite, which may explain some of the hot spots within oil palm estates. This movement strategy may allow for better vigilance as seen on a few occasions when elephants spent 2–5 days in the Bukit Melapi-Yu Kwang Corridor, near the village of Sukau, before leaving the area (Othman, personal observation).Hot spots in the oil palm landscape can also be explained by feeding opportunities, since elephants feed on palm shoots, leaves and hearts73. Elephants are known to eat the shoots of newly planted oil palms, often killing the palms and causing significant economic damages35. Since 2010, many estates located in the Lower Kinabatangan have started a new palm rotation. Palms are replanted every 25 years. A new rotation includes land clearing, bole and root mass removal, and the shredding or chipping of felled palms. Elephants are attracted to the shredded palm hearts since it gives them easy access to one of their favourite food72. This particular behaviour does not cause economic damage, and some estate managers allow the elephants to stay and forage in the chipping areas. This was documented for several collared elephants, whose hot spots and time spent were particularly high within oil palm (e.g. Gading and Sandy, two males; and Ratu and Ita, two females). Once the shredded palms have dried, however, elephants will leave these areas and move elsewhere. Within oil palm estates, some elephants have been found to travel more directly and rapidly suggesting ‘exploratory’ behaviour, which could be associated with searching for young palms or areas of palm felling and chipping of palm hearts15.Lastly, elephants may still be using their historical range that used to be covered with forest before conversion to oil palm. Other factors potentially explaining the relatively high use of oil palm estates include seasonal variations of ranging patterns. Indeed events of drought or floods limit the access to various parts of the floodplain and will tend to confine the animals in some areas9,63.In Sabah the state authorities have recorded at least 200 elephant deaths from the year 2010 to 2021 and most of these have occurred on, or near, oil palm estates14,74,75,76. Deaths from non-natural causes are largely due to poisoning (both accidental and intentional), gunshot wounds, poaching for tusks and other body parts, and snares35. Stopping killing and enabling a safe coexistence between people and elephants within multiple-use landscapes that are dominated by oil palm is one of the key strategies developed in the Bornean Elephant Action Plan for Sabah (2020–2029), which was endorsed by the State14. Based on our results in Lower Kinabatangan, a series of recommendations are proposed.This study underscores the importance of remaining forested areas for the Lower Kinabatangan elephant population. Full protection of all forest fragments left in the Lower Kinabatangan is urgently needed. Several official mechanisms are available to fulfil this request that has been proposed for the past 20 years by various organizations46.The current network of forests available in the Lower Kinabatangan is too small and fragmented to sustain a viable elephant population. Forest corridors must be created across the landscape through reforestation exercises, whilst concurrently undertaking enrichment planting of native understory forage within forested areas as this may minimize the need for elephants to search for easily accessible food in high-risk oil palm landscapes21,22,23.Current governmental plans to build a road bridge and public road/highway linking the southern bank of the Kinabatangan River to Tabin Wildlife Reserve to the south will irreversibly impact the Lower Kinabatangan elephant population by cutting the current range into two isolated parts. This will impact the elephants ranging patterns, potentially even fragmenting the already small population into two groups, and potentially leading to elephant deaths by vehicle collisions (which is becoming increasingly common in Peninsular Malaysia), and increase the risk of poaching activities, all resulting in a decrease in the genetic diversity of the, already small and isolated, population14,67.Eventually, the future of the Kinabatangan elephant population resides in improving land use and management practices within oil palm estates currently used by elephants. We recommend that priority should be given at improving elephant movements in oil palm estates by removing unnecessary man-made barriers and only cautiously installing temporary electric fences to protect sensitive areas. For example, the use of electric fences around mature oil palm and areas whereby palms are being removed and chipped could be prohibited, and electric fences permitted solely for protecting oil palm nurseries, new plantings and young oil palms (e.g. up to 7–8 years old), and staff and office quarters. This would greatly allow for landscape permeability for elephants, and other species that need to cross the landscape for their ecological and biological needs14.A handful of guidelines exist to assist oil palm managers and staff in managing elephant populations in their respective estates72,77. However, there is a need for a more comprehensive set of guidelines, which delineate better practices with the aim to increase the protection of people and elephants outside protected areas. Guidelines should specify “do’s” and “don’ts” (based on best available data and knowledge) of actions needed before, during and after elephants visit oil palm estates and smallholdings.Sabah now is in an interesting transition within their palm oil sector. On the 21st October 2015, the Sabah State Cabinet committed to produce 100% certified sustainable palm oil, by 2025, under the Roundtable for Sustainable palm Oil (RSPO) Jurisdictional Certification approach. Under this approach, areas of High Conservation Value and areas identified within the High Carbon Stock Approach need specific management and monitoring, in order to comply with RSPO principles and criteria78,79,80. Sabah government can use this platform to build an integrated landscape level approach to better manage landscapes within known elephant ranges (which is considered a High Conservation Value species) to allow for a safe and permeable movement through the landscape.Eventually, long-term survival of the Bornean elephant will mainly depend on how people and elephants can co-exist. It is our hope that this study illustrates the importance of protecting all forested habitat and effectively managing areas outside of protected areas to allow for long-term elephant coexistence with humans in this landscape. More

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Ethical statementEthics approval was obtained for this study from the ethics committee of the University of Goettingen (Chair: Prof. Dr. Peter-Tobias Stoll) under the reference number 17./04.22Wurz.Study areaAll plots were situated in northeastern Madagascar in the SAVA region (Supplementary Fig. 1). The natural vegetation is tropical lowland rainforest, but deforestation rates are high30,67.The region is globally and nationally one of the most biodiverse places with high levels of endemism17,68. Forest loss is mainly driven by slash-and-burn shifting hill rice cultivation58. The region is characterized by a warm and humid climate with an annual rainfall of 2255 mm and a mean annual temperature of 23,9 °C (mean value of 60 plots extracted from CHELSA climatology69). Vanilla is the main cash crop in the SAVA region, making Madagascar the main vanilla producer globally21,22. Vanilla prices have shown strong fluctuations over the past years, with a price boom between 2014 and 2019 triggering an expansion of vanilla agroforestry in the region22,23.Study designWe selected 10 villages based on the 60 villages selected within the Diversity Turn in Land Use Science project22 (Supplementary Fig. 1). We selected the villages based on the list of villages for our study region from official election lists which listed all villages within a fokontany individually22. Village boundaries, demographics, infrastructure were defined based on a rapid survey with the village chief. Among the 60 villages, we considered all villages without coconut plantations, with less than 40% water (river, sea, and lakes) to avoid a strong influence of water elements and with forest fragments and shifting cultivation present within a 2 km radius around the village. Two of these 17 villages overlapped within a 2 km radius of the villages, thus we randomly selected one of them, resulting in 14 villages. We visited these 14 villages in a randomized order and stopped after we found 10 villages which fulfilled the necessary criteria (all land-use types present, willing to participate). In each of the 10 villages, we selected three vanilla agroforests, one forest fragment, and two fallows. Overall, we studied 60 plots across 10 villages and 10 plots in one protected old-growth forest (Marojejy National Park). All plots had a minimum distance of 260 m and a mean minimum distance of 794 m (SD = 468 m) to each other. Plot elevation ranged between 10 and 819 m.a.s.l. (mean  = 205 m, SD = 213 m; Supplementary Table 20).Plot selectionIn each of the 10 villages, we selected three vanilla agroforests with low, medium, and high canopy closure, respectively, covering a within village canopy cover gradient. To refine our vanilla agroforest classification, we used interviews with the plot owners to categorize all vanilla agroforests based on land-use history into fallow- and forest-derived agroforests15. Forest-derived vanilla agroforests are established within forest fragments, which have been manually thinned of dense understory vegetation. Fallow-derived vanilla agroforests are established on formerly slashed and burned plots, where vegetation has been cleared for hill rice production (shifting cultivation system locally called tavy). Out of our 30 vanilla agroforests, 20 vanilla agroforests were fallow-derived and 10 vanilla agroforests were forest-derived, roughly matching the proportion of fallow- and forest-derived vanilla agroforests across the study region (70% are fallow-derived vanilla agroforests, 27% are forest-derived vanilla agroforests and 3% of unknown origin22.In addition to vanilla agroforests, we selected one forest fragment in each village. Forest fragments were located inside the agricultural landscape and were remnants of the once continuous forest; these fragments are frequently used for natural product extraction. Forest fragments have not been burned or clear cut in living memory, yet the ongoing resource extraction results in a much simplified stand structure and fewer large trees compared to old-growth forest12. Furthermore, we chose one herbaceous and one woody fallow in each of the 10 study villages. Both fallow types form part of the shifting hill rice production cycle and represent the fallow period at different stages after the crop production. Herbaceous fallows have been slashed and burned multiple times with the last cultivation cycle at the end of 2016, one year prior to the first species data collection in 2017, and thereafter left fallow11. The continuous succession of herbaceous fallows turns them into woody fallows with the domination of woody plants including shrubs, trees, and sometimes bamboo. Our 10 woody fallows have last burned 4–16 years before data collection. In this study, we combine both herbaceous and woody fallows into the category “fallow”. Generally, fallows occur in different forms in the study region. The characteristics of fallows depend on the frequency of past fires and the length of fallow periods in between crop cultivation11. Frequent burning results in a loss of native and woody species and a dominance of exotic species and grasses11. In later fallow cycles, fern species increasingly appear11.Due to the commonly repeated slashing and burning, secondary forests are very rare in the study region. Shifting cultivation prevails in Madagascar70, because it is an important option for people to grow food because means for agricultural intensification are scarce. According to our baseline survey (performed in 60 villages in our study region), 90% of the interviewed farmers grow rice for subsistence in addition to growing vanilla22. Out of this sample, 64% of farmers grow rice in irrigated paddies and 26% of farmers use shifting cultivation.We also studied 10 plots at two sites in Marojejy National Park, the only remaining, continuous old-growth forest at a low altitude in our study area71. We chose accessible old-growth forest plots with a minimum distance of 250 m from the forest edge. Five of the 10 old-growth forest plots were located in Manantenina Valley, the other five old-growth forest plots were situated in the eastern part of Marojejy National Park, called Bangoabe area. Illegal selective logging has occurred in some parts of the park. During our plot selection, we avoided sites with traces of selective logging.Land-use history classificationTo collect information on the land-use history or farm history, interviews with farmers are common72,73. We did interviews with the plot owner. Questions on land-use history were binary (forest-derived or fallow-derived) and did not include information on the detailed land-use history (e.g. frequency of burning, past crop systems). Thus, we consider this selfreported data very reliable. The land-use categorization derived by farmers was confirmed by our visual plot inspections (forest-derived vanilla agroforests do have a quite distinctive vegetation structure compared to fallow-derived vanilla agroforests). Additionally, data on tree species composition and soil characteristics show evident differences between the categories and back up the binary land-use history categorization. Analysis of tree species composition showed that fallow- and forest-derived vanilla agroforests differ significantly in tree species composition12. Soil analysis (see Fig. S9) showed that our fallow-derived vanilla agroforests are associated with fertility-related variables such as an increase in calcium, pH, nitrogen, and phosphorus, which is common after slas-and-burn agriculture74,75.Plot designWe collected species data on plots with a radius of 25 m (1964 m2, 0.1964 ha). We established our circular plots in a homogeneous area of the land-use type or forest. Adjacent land uses were usually different because farmers generally own small-scale land with a mean size of 0.66 ha (mean size of agroforests). We assessed vanilla plant data (yield, vine length, vine age, planting density) on 36 vanilla pieds on each of 30 circular vanilla plots (Supplementary Fig. 8). We defined one vanilla pied (foot in French) as the combination of a vanilla vine and a minimum of one support tree. The 36 vanilla pieds were evenly selected in each of the circular plots based on a sampling protocol to ensure comprehensive and unbiased sampling. We chose vanilla pieds independent of age, length or health condition. We marked the 36 selected vanilla pieds per plot with a unique barcode to assess vanilla yield (April 2018) and other plant health variables on the same plant (not used in this study). However, for 37 vanilla pieds (out of a total of 1080 marked vanilla pieds), the barcodes were lost or unreadable and we selected a new plant closest to the original position (independent of age, length, or condition) and marked it with a new unique barcode. We measured the size of the vanilla agroforest by walking with the agroforest owner and a hand-held GPS device at the perimeter of the plot.Vanilla planting densityWe counted each vanilla pied on each 25 m circular plot by dividing the plot in four-quarter segments. We calculated the area of each 25 m radius plot including slope correction and calculated vanilla planting density (vanilla pieds per hectare) by dividing the number of vanilla pieds by the slope-corrected plot area.Vanilla yieldWe measured yield on 30 vanilla plantations (10 forest-derived vanilla plantations and 20 fallow-derived vanilla plantations); three in each of our 10 study villages. We measured vanilla yield on a total of 36 vanilla pieds between March and April 2018. We assessed the vanilla yield before harvest to ensure an accurate yield assessment due to two reasons. Firstly, vanilla pods are commonly harvested successively due to their differing pollination date and maturity requiring multiple visits over several weeks. Secondly, theft of vanilla pods is commonplace around harvest time. We, therefore, estimated the weight of the on-plant-hanging vanilla pods by measuring pod volume and relating this to a prior established volume–weight correlation. This is possible because vanilla pods only grow in length and width in the first 8 weeks of their development76. Our yield assessment consisted of one interview part with the plot owner and one measurement part. The interview part included questions about the occurrence of theft and early harvest on the plantation. During the measurement part, we assessed the number, diameter, and length of all vanilla pods. We measured vanilla pod length with a ruler starting at the junction of stem and pod until the tip of the pod without considering the bending of the pod. We measured the diameter at the widest part of the pod using a caliper. We firstly calculated pod volume based on the standard volume cylinder formula using the measured diameter (cm) and length (cm): V = πr2h.Secondly, we calculated the weight (g) of each pod by using the linear regression equation (y = bx + a) of a weight–volume correlation of 114 vanilla pods from 114 different agroforests (weight, length, and diameter of these 114 green vanilla was assessed post-harvest in 2017). We calculated the weight of all measured pods of the harvest in 2018 based on the formula:$${{{{{rm{volume}}}}}}={{{{{rm{pi }}}}}}({{{{{rm{diameter}}}}}}({{{{{rm{mm}}}}}})/20)^wedge 2ast {{{{{rm{length}}}}}}({{{{{rm{cm}}}}}})$$Here, we divided the pod diameter (mm) by 20 to obtain the radius and to transform millimeters to centimeters. Weight was defined as volume*0.5662 + 0.9699. No vanilla pods were stolen or already harvested on our 36 vanilla pieds and hence we did not need to account for it in our vanilla yield calculation.Vanilla vine lengthWe assessed vanilla vine length for all 36 vanilla pieds (same vanilla pieds as used for the yield assessment) on each plot by measuring the total length of the vine from the lowest to the highest part with a measuring stick. If the vanilla vine was looped on the support tree (= vanilla vine is hanging in multiple loops on the support tree), we measured from the top height of the looping of the vanilla vine until the lowest height of the vine. At the medium height of the vanilla vine, we counted the number of times the vanilla vine passed through. We calculated the total length of the liana by multiplying the maximum height of the vanilla vine by the number of times the vine passed through the middle. In some cases, the vanilla vine looped at two different heights, we thus considered the middle between the two looping heights as the top height. If vanilla vines grew on two different support trees, we considered them as one vanilla pieds if support trees were More