Assessing the distribution and diversity of terrestrial and semi-aquatic mammals is fundamental for effective conservation efforts. Environmental DNA (eDNA) metabarcoding has emerged as a rapid and cost-effective method for surveying mammals. It has promising avenues for conducting national surveys and enabling comprehensive assessments of mammalian populations across diverse habitats. We collected eDNA samples from 60 water systems across six regions in England (from north to south), United Kingdom, over a period of up to four days in each region. We detected 26 mammals from five taxonomic orders across all sampling locations, recovering 53–89

ABSTRACT Environmental DNA (eDNA) metabarcoding has emerged as a promising tool for monitoring fish diversity in a range of diverse aquatic realms. However, eDNA‐based monitoring of fish communities found in hydroelectric dam reservoirs has received relatively limited attention, especially in megadiverse regions such as the Neotropics. Herein, we evaluate eDNA metabarcoding as a biodiversity monitoring tool together with capture‐based fishing methods, in order to compare their efficacy and analyze their complementarity in the characterization of Neotropical fish communities. We obtained 147 water samples from three different sampling sites across the Irapé hydroelectric power plant reservoir (IRR) in Brazil across eight sampling events over 3 years (2019–2021). The 12S mitochondrial ribosomal RNA marker (~170 bp) was amplified and, using a curated reference library, the sequences were assigned to 115 Molecular Operational Taxonomic Units (MOTUs) corresponding to 30 taxa, 20 of which were identified to the species level. Gillnet sampling captured 484 individuals, representing 14 species, with Characiformes dominating the catches and the invasive Serrasalmus brandtii accounting for 68.8% of individuals. Environmental DNA consistently detected greater species richness across the sites and years, including 23 exclusive taxa not detected using gillnets. Beta diversity was high for both methods (β > 0.93), driven mainly by species turnover. Nevertheless, redundancy analysis revealed distinct assemblage structures between methods, and no significant correlation was found between catch‐per‐unit‐effort and eDNA read abundance. These results underscore that when integrated with traditional methods, eDNA enhances biodiversity assessments and supports more comprehensive and cost‐effective monitoring programs in freshwater systems impacted by hydropower development.

ABSTRACT Aquatic ecosystems have been in an alarming state of decline for decades. In particular, estuarine ecosystems have experienced long‐term declines in fish diversity due to factors such as habitat degradation, pollution and altered hydrology. Monitoring these systems is often limited by the difficulty and cost of conventional survey methods. In this study, we applied environmental DNA (eDNA) metabarcoding to assess fish diversity in the Mersey Estuary (UK), a historically severely impacted system. Monthly water samples were collected over a year (2023–2024) across saline, brackish, and freshwater zones. Overall, 69 species were detected, surpassing both historical (46 species) and recent (39 species) records. Richness was highest in the upper freshwater zones, and several species were recorded returning to the estuary for the first time since pre‐industrial times (∼1850s). Peak species richness occurred during winter (December–February). Species composition varied monthly and spatially, though not consistently by season. Approximately 15% of detected species were diadromous, with the endangered Atlantic salmon (Salmo salar) being frequently detected during its key spawning period (October–December), for example. The results presented here indicate a resurgence in estuarine fish diversity in the Mersey and highlight eDNA metabarcoding as a rapid, sensitive tool for monitoring both contemporary and historically absent species, supporting conservation and restoration efforts.

Terrestrial and semi‐aquatic mammals are facing increasing threats globally, highlighting the need for reliable data on species' occurrence, distribution, and abundance for effective conservation efforts. However, obtaining reliable and robust information over broad spatial and temporal scales remains a significant challenge. Environmental DNA (eDNA) and invertebrate‐derived DNA (iDNA) applications have emerged as powerful surveying methods, with the potential to revolutionise ecological monitoring by improving species detections and providing better insights into mammalian distribution and diversity. While eDNA relies on genetic material shed by species into their surroundings, iDNA leverages DNA from invertebrates that interact with mammals. Both approaches offer a cost‐effective means to obtain species records and community diversity metrics. This review explores global applications of e/iDNA for surveying terrestrial and semi‐aquatic mammals. By providing a comprehensive overview of the applications, sampling design, challenges, and prospects, this review serves as a guide to researchers and conservationists seeking to use eDNA for mammalian conservation efforts. By evaluating the current state of e/iDNA applications, this review identifies the challenges and milestones that need to be addressed for these methods to become a practical method for monitoring mammals on a global scale. It highlights the need for further research to enhance the sensitivity and reliability of e/iDNA detections, standardisation of methodologies, and validation through comparison with traditional monitoring methods. This review sheds light on the potential of e/iDNA as valuable tools for aiding mammal conservation and inspiring future research and advancements in this field.

Obtaining accurate population measures of endangered species is critical for effective conservation and management actions and to evaluate their success over time. However, determining the population size and demographic composition of most canopy forest-dwelling species has proven to be challenging. Here, we apply two non-invasive biomonitoring methods, arboreal camera trap and genetic tagging of fecal samples, to estimate the population size of a critically endangered primate, the northern muriqui (Brachyteles hypoxanthus), in the Capara & oacute; National Park, Brazil. When comparing group sizes between camera trapping and genetic tagging, the genetic tagging survey estimated fewer individuals for one of the muriqui groups studied but showed slightly higher population size estimates for the other group. In terms of the cost-efficiency of both methods, arboreal camera trapping had high initial costs but was more cost-effective in the long term. Genetic tagging, on the other hand, did not require expensive equipment for data collection but had higher associated expenses for laboratory consumables and data processing. We recommend the use of both methods for northern muriqui monitoring and provide suggestions for improving the implementation of these non-invasive methods for future routine monitoring. Our findings also highlight the potential of arboreal camera trapping and genetic tagging for other arboreal mammals in tropical forests.

ABSTRACT: Global arthropod populations are changing due to the combined impacts of climate change, land-use transformation, globalisation and trade. These changes can potentially result in the decline and extinction of some native and/or endemic arthropod species, while other species that potentially pose threats to human and animal populations may increase. Such dynamics lead to weakened ecosystem resilience, which can facilitate the establishment and spread of species with vector capacities, such as mosquitoes. While many of the mosquito species present in Ireland possess vector capacities, populations have not been extensively surveyed since 1991. A follow-up investigation into Irish mosquito species presence was performed in 2024. At that time of the 1991 study, species identification relied on morphological examination, a method that even then was recognised as inadequate for differentiating certain species within complexes; the 2024 follow-up study employed both morphological and genetics methods for species identification. In this study we conduct the first investigation of Irish mosquito populations using DNA barcoding of two genetic regions to confirm species presence. Our results confirmed the presence of species recently and not previously recorded from Ireland, including Culex torrentium and Culex pipiens s.s. ( sensu stricto ). We demonstrate that barcoding with Cytochrome C Oxidase Subunit 1-based primers is suitable for most species-level identifications. However, additional primer sets targeting the Internal Transcribed Spacer regions 1 and 2 were necessary to differentiate species within the Culex pipiens complex, although we found that researchers should be cautious relying on genetic reference databases such as GenBank for this purpose. Nevertheless, the multi-locus approach employed in this study can enhance national surveillance efforts, especially in monitoring mosquitoes that may transmit vector-borne diseases, and in recognising increased species diversity from a biodiversity perspective.

Great Britain has three native shrews, while the greater white-toothed shrew (GWT: Crocidura russula) is native to the European continent and some Channel islands. The GWT shrew was first reported in northern England in 2022. We detail its immediate investigation through national authorities, non-government bodies and individuals. Sixteen GWT were among 595 small mammals live-trapped. Barn owl pellet analysis revealed 56 GWT skulls in two areas. Genetic analysis of the cytochrome b gene suggests these population were derived from one or more continental European introductions, but not from the nearby island of Ireland where this non-native species has been present since at least 2007. The overall government response from the Department for Environment, Food and Rural Affairs and Natural England concluded that the species is too widespread to have any reasonable chance of eradication, but there remain ongoing efforts to determine the extent of invasion and its effect on native species.

Environmental DNA (eDNA)-based monitoring has become an established and efficient method for surveying biodiversity in aquatic systems. However, there is a need to compare and standardize sampling methods across different ecosystem types, particularly complex ecosystems such as estuaries, where unique challenges exist for monitoring fish populations due to fluctuating environmental factors. Here, we compare species richness obtained from eDNA metabarcoding data using four different eDNA filtration methods: three manual filtration methods with different pore sizes (0.45, 1.2, and 5 mu m) and a newly established passive method, the metaprobe. The study was applied across a salinity gradient in a hyper-tidal estuarine ecosystem. Overall, 44 fish species were detected across the four methods used. The 0.45 mu m filter recovered the highest richness (39 species), then the metaprobe method (35), followed by the 1.2 mu m (34) and 5 mu m (33) filters. Filter performance between salinity gradients revealed that the 0.45 mu m and the 1.2 mu m methods recovered the highest species richness across all sampled zones. The 0.45 mu m also had the most consistent detection probabilities using representative species from each zone. While the 0.45 mu m method appeared to be the optimal method, each of the methods can be considered a viable and comparable option for biomonitoring in dynamic ecosystems such as estuaries and rivers. In particular, the passive metaprobe (used in a freshwater system for the first time here) performed well in comparison to the manual filtering methods despite a short deployment time. This study provides critical insights for optimizing fish diversity assessments using eDNA metabarcoding in estuarine ecosystems, providing a valuable framework for future monitoring efforts in similar systems worldwide.

Mesophotic Coral Ecosystems (MCEs) occur in the middle to lower photic zone (~30 to 150 m) of tropical and subtropical regions, are often extensions of shallow reef communities, and generally hold great importance for local commercial fisheries. Compared to their shallower counterpart, MCEs have been traditionally understudied, primarily due to their inaccessibility with traditional monitoring methodologies. In this study, we aim to provide an interdisciplinary assessment of the biodiversity of Bermudan reef fish communities from the upper/lower mesophotic interface (60 m) by utilising a combination of environmental DNA (eDNA) metabarcoding and baited remote underwater videos (BRUVs). In total, 155 species from 137 genera were detected by eDNA metabarcoding whilst a total of 85 species from 53 genera were detected by BRUVs. The combined species detections totalled 182 species with approximately half of those detections unique to this study when compared to previous studies. Both methodologies found differences in alpha diversity between study locations, with each method independently detecting the highest species richness at the same location. The species assemblage at each location was dominated (~80%) by species known to occur throughout the shallow reef system and the upper mesophotic, whilst species only known to inhabit mesophotic ecosystems accounted for ~6% at each location. These findings suggest a high level of species continuity with the adjacent shallower reef systems. The complementary nature of eDNA metabarcoding and BRUVs allows for a more accurate characterisation of fish biodiversity at the upper/lower mesophotic interface, which can lead to a more comprehensive understanding of ecosystem structure and more informed management decisions. ### Competing Interest Statement The authors have declared no competing interest.

Leptospirosis is a complex and often underestimated global bacterial disease that continues to be of zoonotic concern. It is difficult to diagnose and has an unclear pathogenesis. Several new species of the genus Leptospira have been discovered in recent years; the impact of these species on animal health is unknown. In 2013, Leptospira tipperaryensis was first identified in greater white-toothed shrews (GWTSs, Crocidura russula) in Ireland, where they are an invasive species that displaces the native pygmy shrew (Sorex minutus). This study investigated the prevalence of Leptospira spp., including L. tipperaryensis, and their potential impact on the health of shrews from Ireland using histopathology (n=212), immunohistochemistry (IHC; n=206), and quantitative PCR (n=168) on renal tissues. Shrews (n=81) from Belle Île, France were examined as a species and habitat control group using histopathology (n=81) and IHC (n=79). No Leptospira were detected with any of the methods in renal tissues from shrews sampled in Ireland and there was no significant renal pathology. In contrast, 34.6% (28/81) of shrews from Belle Île were positive on IHC for Leptospira sp. and had associated chronic nephritis in histopathology. The results do not indicate a negative impact by L. tipperaryensis or other Leptospira spp. on the health and distribution of the GWTS and the pygmy shrew in Ireland; onward transmission within the shrew population currently appears unlikely.

Citizen scientists have become integral participants in biodiversity monitoring, and the demand for effective surveying efforts has sparked interest in utilizing environmental DNA (eDNA) for species monitoring, drawing volunteers into survey planning and sample collection. However, there remains a gap in understanding the motivations behind volunteer engagement in surveys that don’t involve direct observations of species, including the need to validate collected data and recognize volunteer contributions to ensure their satisfaction. To address this gap, we used questionnaires to assess volunteer science capital, motivation to participate, and their experiences during eDNA sampling. We trained ten conservation volunteers, all of whom were members of the Essex Wildlife Trust, to collect eDNA samples from two rivers and a beaver enclosure to detect terrestrial and semi-aquatic mammals. Citizen scientists were highly motivated and demonstrated high science capital, enabling them to develop innovative eDNA sampling methods and take enjoyment in contributing to meaningful scientific knowledge and helping their local wildlife. Additionally, citizen scientists detected more species compared with eDNA researchers, underscoring the value of local knowledge, and the longer sampling periods associated with typical citizen scientist projects. This case study highlights the benefits of involving citizen scientists in eDNA surveys, as sharing results led to meaningful discussions about the species detected and further enriched knowledge exchange. The case study’s limitations include small sample size and limited participant diversity in terms of age, gender, and ethnicity. However, the findings can inform future research with larger and more diverse participants.

Sex chromosomes differ in their inheritance properties from autosomes and hence may encode complementary information about past demographic events. We compiled and analyzed a range-wide resequencing data set of the red deer (Cervus elaphus), one of the few Eurasian herbivores of the Late Pleistocene megafauna still found throughout much of its historic range. Our analyses of 144 whole genomes reveal striking discrepancies between the population clusters suggested by autosomal and X-chromosomal data. We postulate that the genetic legacy of Late Glacial population structure is better captured and preserved by the X chromosome than by autosomes, for two reasons. First, X chromosomes have a lower Ne and hence lose genetic variation faster during isolation in glacial refugia, causing increased population differentiation. Second, following postglacial recolonization and secondary contact, immigrant males pass on their X chromosomes to female offspring only, which effectively halves the migration rate when gene flow is male mediated. Our study illustrates how a comparison between autosomal and sex chromosomal phylogeographic signals unravels past demographic processes that otherwise would remain hidden.

Increasing reports of zoonotic avian influenza virus (AIV) spillovers to mammals signal critical shift in their ecology and raise substantial public health concerns. The highly pathogenic avian influenza H5N1 clade 2.3.4.4b has driven this expansion, with genetic adaptations enhancing replication in mammalian hosts. Adaptations have been identified in diverse carnivore species, including American mink ( Neogale vison ), red foxes ( Vulpes vulpes ), and otters ( Lutra lutra ). These carnivores often feed on, or share habitat with, wild birds, making them suitable species for monitoring AIV presence in mammals. Here we investigated exposure to influenza A viruses (IAVs), including H5 and H7 subtypes in three mesocarnivore species (red foxes, American mink, and European badgers) in Ireland. Using enzyme-linked immunosorbent assays, we detected a seroprevalence for IAVs of 24.6% (28/114) in foxes, 22.2% (2/9) in mink, and 1% (1/96) in badgers. Among red fox samples positive for antibodies against IAVs, 82.1% (23/28) were positive for antibodies against the H5 subtype. No antibodies against the H7 subtype were detected. We also examined the use of Nobuto filter paper as a reliable alternative to serum samples for IAVs antibody detection via ELISA and assessed the use of haemolysed serum samples. These findings, as well as those gathered from ongoing passive surveillance of wild birds, highlight that influenza A is circulating in wildlife in Ireland. If we are to better understand influenza A dynamics in Ireland, and globally, it is imperative that surveillance programmes are supported, and serosurveys provide one valuable tool for active surveillance.

.-Batrachochytrium salamandrivorans (Bsal) fungus has the potential to cause high mortality rates in some European salamanders and newts (urodelans) and is in the process of expanding its invasive range in Europe. Therefore, monitoring its distribution and better understanding both the species threatened and the mechanics of infection are essential in mitigating damage Bsal may cause. Environmental DNA has emerged as a promising noninvasive method for detecting both this fungal pathogen and amphibian communities in infected areas. We applied these methods in the province of Gelderland, Netherlands, where the pathogen has previously been detected and is expanding its range, with the goal of characterizing the natural amphibian community present. We sampled 27 bodies of water in the region surrounding the known outbreak sites, determined the presence or absence of Bsal using a targeted quantitative polymerase chain reaction assay, and applied an environmental DNA metabarcoding approach to characterize the amphibian communities using two different primer sets. The 12S vertebrate primer set outperformed the 16S amphibian primer set and detected all expected amphibians in the study area: Bufo bufo, Lissotriton vulgaris, Pelobates fuscus, Pelophylax spp., Rana temporaria and Triturus cristatus. Bsal was detected at 8 of 27 ponds. A distance-based redundancy analysis found a weak but significant relationship between Bsal presence and composition of amphibian communities. This study may provide a basis for future studies on Bsal and its relationship with amphibian communities in Europe, highlighting the need for further research into mechanisms of persistence and transmission between bodies of water.

Genome-wide technologies open up new possibilities to clarify questions on genetic structure and phylogeographic history of taxa previously studied with microsatellite loci and mitochondrial sequences. Here, we used 736 individual red deer (Cervus elaphus) samples genotyped at 35,701 single nucleotide polymorphism loci (SNPs) to assess the population structure of the species throughout Europe. The results identified 28 populations, with higher degrees of genetic distinction in peripheral compared to mainland populations. Iberian red deer show high genetic differentiation, with lineages in Western and Central Iberia maintaining their distinctiveness, which supports separate refugial ranges within Iberia along with little recent connection between Iberian and the remaining Western European populations. The Norwegian population exhibited the lowest variability and the largest allele frequency differences from mainland European populations, compatible with a history of bottlenecks and drift during post-glacial colonization from southern refugia. Scottish populations showed high genetic distance from the mainland but high levels of diversity. Hybrid zones were found between Eastern and Western European lineages in Central Europe as well as in the Pyrenees, where red deer from France are in close contact with Iberian red deer. Anthropogenic restocking has promoted the Pyrenean contact zone, admixture events in populations on the Isle of Rum and in the Netherlands, and at least partly the admixture of the two main lineages in central-eastern Europe. Our analysis enabled detailed resolution of population structure of a large mammal widely distributed throughout Europe and contributes to resolving the evolutionary history, which can also inform conservation and management policies.

The Northern muriqui ( Brachyteles hypoxanthus ) is one of the world's most critically endangered primates, with only ~1000 mature individuals remaining in the wild. Habitat loss and hunting have led to its sharp decline, making conservation efforts crucial. Analyses of gut microbiomes in wild populations can provide valuable information on host health and vulnerability, and ultimately, contribute to baseline knowledge toward improving conservation programs and reintroduction efforts. In this study, we analyzed the microbiome (16S rRNA metabarcoding) of fecal samples belonging to 53 uniquely genotyped individuals from three social groups from the Caparaó National Park, aiming to provide the first assessment of the microbiome diversity and composition for this species. Our results showed the muriqui gut microbiome was predominantly composed of the phyla Bacteroidetes and Firmicutes, with the dominant classes represented by Bacteroidia and Clostridia. High similarity in bacterial diversity and composition was found for individuals from distinct groups, suggesting a negligible geographical effect at the fine spatial scale analyzed. No significant effect of host genotype heterozygosity levels on microbiota diversity was recovered, but a significant influence of genetic distance on microbiota community structure and composition was demonstrated. Our findings stress the importance of considering associations between host genetics and the microbiome and suggest that the analyzed populations host a similar microbiome composition. This detailed microbiome assessment can aid conservation actions, including future anthropogenic impact assessments and animal reintroductions.

Environmental DNA (eDNA) has become an established and efficient method for monitoring biodiversity in aquatic systems. However, there is a need to compare and standardise sampling methods across ecosystem types, particularly complex ecosystems such as estuaries where unique challenges for monitoring fish populations are present due to fluctuating environmental factors. Here, we compare fish biodiversity metrics obtained from eDNA metabarcoding data using four different eDNA filtering methods: three manual filtering methods with different pore sizes (0.45, 1.2 and 5 µm) and a newly established passive method, the metaprobe. The study was applied across a salinity gradient in a hyper-tidal estuarine ecosystem. Overall, 44 fish species were detected across the four methods used. The 0.45 µm filter recovered the highest richness (39 species), then the metaprobe method (35), followed by the 1.2 µm (34) and 5 µm (33) filters. Filter performance between salinity gradients revealed that the 0.45 µm and the 1.2 µm methods recovered the highest species richness across all sampled zones. The 0.45 µm also had the most consistent detection probabilities using representative species from each zone. While the 0.45 µm method appeared to be the optimal method, each of the methods can be considered as a viable and comparable option for biomonitoring in dynamic ecosystems such as estuaries and rivers. In particular, the passive metaprobe (used in a freshwater system for the first time here) performed well in comparison to the manual filtering methods despite a short deployment time. This study provides critical insights for optimising fish biodiversity assessments using eDNA metabarcoding in estuarine ecosystems, providing a valuable framework for future monitoring efforts in similar systems worldwide. ### Competing Interest Statement The authors have declared no competing interest.

Monitoring is essential to ensure that environmental goals are being achieved, including those of sustainable agriculture. Growing interest in environmental monitoring provides an opportunity to improve monitoring practices. Approaches that directly monitor land cover change and biodiversity annually by coupling the wall-to-wall coverage from remote sensing and the site-specific community composition from environmental DNA (eDNA) can provide timely, relevant results for parties interested in the success of sustainable agricultural practices. To ensure that the measured impacts are due to the environmental projects and not exogenous factors, sites where projects have been implemented should be benchmarked against counterfactuals (no project) and control (natural habitat) sites. Results can then be used to calculate diverse sets of indicators customized to monitor different projects. Here, we report on our experience developing and applying one such approach to assess the impact of shaded cocoa projects implemented by the Instituto de Manejo e Certificação Florestal e Agrícola (IMAFLORA) near São Félix do Xingu, in Pará, Brazil. We used the Continuous Degradation Detection (CODED) and LandTrendr algorithms to create a remote sensing-based assessment of forest disturbance and regeneration, estimate carbon sequestration, and changes in essential habitats. We coupled these remote sensing methods with eDNA analyses using arthropod-targeted primers by collecting soil samples from intervention and counterfactual pasture field sites and a control secondary forest. We used a custom set of indicators from the pilot application of a coupled monitoring framework called TerraBio. Our results suggest that, due to IMAFLORA's shaded cocoa projects, over 400 acres were restored in the intervention area and the community composition of arthropods in shaded cocoa is closer to second-growth forests than that of pastures. In reviewing the coupled approach, we found multiple aspects worked well, and we conclude by presenting multiple lessons learned.

Aim: The central and western Amazonia underwent several landscape changes during the Quaternary. Whereas the Riverine Barrier Hypothesis is traditionally used to explain the influence of rivers on speciation, processes such as river rearrangements have been overlooked to explain the geographic distribution and evolutionary history of Amazonia biota. Here, we tested how river rearrangements influenced the evolutionary history of uakari monkeys, genus Cacajao, a primate genus primarily associated with seasonally flooded forests in central and western Amazonia. Location: Central and Western Amazonia. Taxon: The genus Cacajao, including the black uakaris (C. melanocephalus, C. ayresi, C. hosomi); and the bald-headed uakaris (C. calvus, C. amuna, C. rubicundus, C. ucayalii, C. novaesi). Methods: We performed a continuous phylogeographic analysis using 77 cytochrome b sequences to identify the origin and dispersal of Cacajao lineages. We used genome-wide SNP variation (ddRADseq) to investigate population structure, gene flow and demographic history in Cacajao populations and used digital elevation models to identify landscape and riverscape characteristics that may have influenced the geographic distribution of Cacajao. Results: Our continuous phylogeographic reconstruction pointed out that the ancestral Cacajao lineage occupied the flooded forests of the Solimoes River, in central Amazonia, at similar to 1.7 Mya and descendant lineages dispersed throughout central and western Amazonia more recently. We identified gene flow in both black and bald-headed uakari populations, even across rivers considered barriers (e.g. the Negro River). Landscape analysis showed that river rearrangements influenced the geographic distribution and population structure in Cacajao. Historical demographic analyses suggest varied scenarios of population size changes among Cacajao monkeys consistent with periods of intense dynamism in flooded habitats and the formation of non-flooded upland forests. Main Conclusion: Our results support that the river rearrangements have shaped the geographic distribution and divergence of recently diverged Cacajao lineages. Landscape and riverscape changes, along with retractions of the flooded forests, isolated some Cacajao populations in floodplain areas. Our study also suggests that these events led to the recent changes in demographic histories in species with a restricted geographic distribution.

Obtaining accurate population measures of endangered species is critical for effective conservation and management actions and to evaluate their success overtime. However, determining the population size and demographic composition of most canopy forest-dwelling species has proven to be challenging. Here, we apply two non-invasive biomonitoring methods, arboreal camera trap and genetic tagging of faecal samples, to estimate the population size of a critically endangered primate, the northern muriqui (Brachyteles hypoxanthus), in the Caparao National Park, Brazil. When comparing population sizes between camera trapping and genetic tagging, the genetic tagging survey estimated fewer individuals for one of the muriqui groups studied but showed slightly higher population size estimates for the other group. In terms of the cost-efficiency of both methods, arboreal camera trapping had high initial costs but was more cost-effective in the long-term. Genetic tagging on the other hand did not require expensive equipment for data collection but had higher associated expenses for laboratory consumables and data processing. We recommend the use of both methods for northern muriqui monitoring and provide suggestions for improving the implementation of these non-invasive methods for future routine monitoring. Our findings also highlight the potential of arboreal camera trapping and genetic tagging to other arboreal mammals in tropical forests. ### Competing Interest Statement The authors have declared no competing interest.