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Primates are one of the most threatened groups of mammals. Understanding their patterns of population occurrence and abundance, especially in response to threats, is critical for informing conservation action. The crested black macaqueMacaca nigrais the only Critically Endangered species of Sulawesi's seven endemic macaques. Little is known about its distribution or its response to deforestation and hunting. We conducted a camera-trap survey across the entire species range using an occupancy-based analytical approach to (1) establish the first range-wide baseline of occurrence, (2) investigate how environmental and anthropogenic factors influence occurrence, (3) identify priority conservation subpopulations, and (4) test the efficacy of the sampling and analytical protocol for temporal monitoring ofM. nigrausing occupancy as the state variable. From 9,753 camera-trap days,M. nigrawas detected on 473 days at 77 of the 111 camera locations. Species occupancy was 0.66 and highest inside protected areas and closed canopy forest. We identified eight distinct subpopulations, based on distribution and forest fragment size. To inform future monitoring, we used a power analysis to determine if our effort would allow us to detect inter-annual occupancy declines of 10%, and found that 90 camera locations surveyed for 3 months (8,100 camera days) across three consecutive seasons is the effort required to detect such change with 80% certainty. Our study underscores the importance of well-managed protected areas and intact forests for the long-term survival of the crested black macaque, and tests the effectiveness of camera traps to monitor primates at the landscape scale.

Outbreaks of emerging infectious diseases are trained by local biotic and abiotic factors, with host declines occurring when conditions favour the pathogen. Extinction of the Tanzanian Kihansi spray toad (Nectophrynoides asperginis) in 2004 was contemporaneous with the construction of a dam, implicating habitat modification in the loss of this species. However, high burdens of a globally emerging infection, Batrachochytrium dendrobatidis (Bd) were synchronously observed implicating infectious disease in this toads extinction. Here, by shotgun sequencing skin DNA from archived toad mortalities and assembling chytrid mitogenomes, we prove this outbreak was caused by the BdCAPE lineage and not the panzootic lineage BdGPL that is widely associated with global amphibian extinctions. Molecular dating showed an invasion of BdCAPE across Southern Africa overlapping with the timing of the extinction event. However, post-outbreak surveillance of conspecific species inhabiting this mountainous region showed widespread infection by BdCAPE yet no signs of amphibian ill-health or species decline. Our findings show that despite efforts to mitigate the environmental impact caused by dams construction, invasion of the pathogen ultimately led to the loss of the Kihansi spray toad; a synergism between emerging infectious disease and environmental change that likely heralds wider negative impacts on biodiversity in the Anthropocene.

Evidence-based decision-making is most effective with comprehensive access to scientific studies. If studies face significant publication delays or barriers, the useful information they contain may not reach decision-makers in a timely manner. This represents a potential problem for mission-oriented disciplines where access to the latest data is required to ensure effective actions are undertaken. We sought to analyse the severity of publication delay in conservation science—a field that requires urgent action to prevent the loss of biodiversity. We used the Conservation Evidence database to assess the length of publication delay (time from finishing data collection to publication) in the literature that tests the effectiveness of conservation interventions. From 7,447 peer-reviewed and non-peer-reviewed studies of conservation interventions published over eleven decades, we find that the raw mean publication delay was 3.2 years (±2SD = 0.1) and varied by conservation subject. A significantly shorter delay was observed for studies focused on Bee Conservation, Sustainable Aquaculture, Management of Captive Animals, Amphibian Conservation, and Control of Freshwater Invasive Species (Estimated Marginal Mean range from 1.4–1.9 years). Publication delay was significantly shorter for the non-peer-reviewed literature (Estimated Marginal Mean delay of 1.9 years ± 0.2) compared to the peer-reviewed literature (i.e., scientific journals; Estimated Marginal Mean delay of 3.0 years ± 0.1). We found publication delay has significantly increased over time (an increase of ~1.2 years from 1912 (1.4 years ± 0.2) to 2020 (2.6 years ± 0.1)), but this change was much weaker and non-significant post-2000s; we found no evidence for any decline. There was also no evidence that studies on more threatened species were subject to a shorter delay—indeed, the contrary was true for mammals, and to a lesser extent for birds. We suggest a range of possible ways in which scientists, funders, publishers, and practitioners can work together to reduce delays at each stage of the publication process.

Primates are among the most threatened taxa of mammals in the world. Tracking the status of primates requires continually assessing population distribution, abundance, and threats, which in turn requires the extent of a species’ occurrence to be known. Defining this important parameter in practice can be difficult. In this article we demonstrate how camera traps can be used to address this with a case study involving two macaque species on the northernmost peninsula of Sulawesi, Indonesia. We deployed 83 camera traps across the suspected interface between the Critically Endangered Macaca nigra and the Vulnerable Macaca nigrescens. Using spatially explicit photographic records of both species, we found the boundary between the two species is 14.85 km farther west than previously defined. We estimate that the additional area encompassed by this new boundary location equates to 224 km2 of suitable habitat for M. nigra, an increase of 7.5%. This has important implications for more accurately assessing the threatened status of both species in the future. As camera traps become cheaper, their deployment at broader spatial scales is becoming more feasible, which in turn provides opportunities to enhance our ecological understanding of species. Here, we demonstrate an additional insight that can be gained from such technology, by showing how the range extent of a Critically Endangered primate can be accurately demarcated. Accordingly, we encourage primatologists to think more broadly about the possible applications of camera traps and to include them as tools in their conservation inventories.

Evidence-based decision making is most effective with comprehensive access to scientific studies. If studies face delays or barriers to being published, the useful information they contain may not reach decision-makers in a timely manner. This represents a potential problem for mission-oriented disciplines where access to the latest data is paramount to ensure effective actions are deployed. We sought to analyse the severity of publication delay in conservation science — a field that requires urgent action to prevent the loss of biodiversity. We used the Conservation Evidence database to assess the length of publication delay (time from finishing data collection to publication) in the literature that tests the effectiveness of conservation interventions. From 7,415 peer-reviewed and non-peer-reviewed studies of conservation interventions published over eleven decades, we find that the mean publication delay (time from completing data collection to publication) was 3.6 years and varied by conservation subject — a smaller delay was observed for studies focussed on the management of captive animals. Publication delay was significantly smaller for studies in the non-journal literature (typically non-peer-reviewed) compared to studies published in scientific journals. Although we found publication delay has marginally increased over time (1912-2020), this change was weak post-1980s. Publication delay also varied inconsistently between studies on species with different IUCN Red List statuses and there was little evidence that studies on more threatened species were subject to a smaller delay. We discuss the possible drivers of publication delay and present suggestions for scientists, funders, publishers, and practitioners to reduce the time taken to publish studies. Although our recommendations are aimed at conservation science, they are highly relevant to other mission-driven disciplines where the rapid dissemination of scientific findings is important.

Summary The fungus Batrachochytrium dendrobatidis (Bd) causes chytridiomycosis, a lethal epizootic disease of amphibians. Rapid identification of the pathogen and biosecurity is essential to prevent its spread, but current laboratory‐based tests are time‐consuming and require specialist equipment. Here, we describe the generation of an IgM monoclonal antibody (mAb), 5C4, specific to Bd as well as the related salamander and newt pathogen Batrachochytrium salamandrivorans (Bsal). The mAb, which binds to a glycoprotein antigen present on the surface of zoospores, sporangia and zoosporangia, was used to develop a lateral‐flow assay (LFA) for rapid (15 min) detection of the pathogens. The LFA detects known lineages of Bd and also Bsal, as well as the closely related fungus Homolaphlyctis polyrhiza, but does not detect a wide range of related and unrelated fungi and oomycetes likely to be present in amphibian habitats. When combined with a simple swabbing procedure, the LFA was 100% accurate in detecting the water‐soluble 5C4 antigen present in skin, foot and pelvic samples from frogs, newts and salamanders naturally infected with Bd or Bsal. Our results demonstrate the potential of the portable LFA as a rapid qualitative assay for tracking these amphibian pathogens and as an adjunct test to nucleic acid‐based detection methods.

There are two PFS for this article, one is the original article and the other is an Erratum specifying the errors in the original article. In comparison to other ecosystems in east Africa, the biodiversity of the coastal forests of Kenya’s northern coastline is poorly documented, even in the case of large terrestrial mammals. In response to this, we undertook a systematic survey of the Boni-Dodori forests using four camera trap grids with camera spacing of 2 km covering 300 km 2 over 7020 camera trap days. We recorded 37 mammal species and derived camera trap rates and estimated occupancy for 31 medium-to-large terrestrial species, some of which represent range extensions. Remarkably, the critically endangered Aders’ duiker was the most frequently recorded species. A distinctive form of giant sengi and the vulnerable Sokoke bushy-tailed mongoose were also widely distributed and relatively abundant. Other significant records of threatened species included African wild dog, African lion and Pousargues’s monkey. Species richness and relative abundance of all species were higher than that recorded for Arabuko-Sokoke Forest, Kenya’s only other large coastal forest, using the same camera trap survey protocol. Keywords : Boni-Dodori forest, coastal forest, camera trapping, mammals, species richness, trap rates, occupancy

Zoos have played a pivotal role in the successful reinforcement and reintroduction of species threatened with extinction, but prioritization is required in the face of increasing need and limited capacity. One means of prioritizing between species of equal threat status when establishing new breeding programs is the consideration of evolutionary distinctness (ED). More distinct species have fewer close relatives such that their extinction would result in a greater overall loss to the Tree of Life. Considering global ex situ holdings of birds (a group with a complete and well-detailed evolutionary tree), we investigate the representation of at-risk and highly evolutionarily distinct species in global zoo holdings. We identified a total of 2,236 bird species indicated by the Zoological Information Management System as being held in zoological institutions worldwide. As previously reported, imperiled species (defined as those possessing endangered or critically endangered threat status) in this database are less likely to be held in zoos than non-imperiled species. However, we find that species possessing ED scores within the top 10% of all bird species are more likely to be held in zoos than other species, possibly because they possess unique characteristics that have historically made them popular exhibits. To assist with the selection of high priority ED species for future zoo conservation programs, we provide a list of imperiled species currently not held in zoos, ranked by ED. This list highlights species representing particular priorities for ex situ conservation planners, and represents a practical tool for improving the conservation value of zoological collections.

Aders’ duiker Cephalophus adersi is a critically endangered small antelope endemic to the coastal forests of east Africa. Threatened by habitat loss and hunting, the species was until recently known to persist only on Zanzibar, Tanzania, and in the Arabuko-Sokoke National Reserve, Kenya. However, more recent observations, have confirmed the occurrence of Aders’ duiker in Kenyan coastal forests north of the Tana River. This paper reports systematic camera trapping results for three sites in the Boni–Dodori coastal forest system north of the Tana and the only other known mainland site for Aders’ duiker, the Arabuko-Sokoke forest. From a total survey effort of 5,723 camera trap days, we demonstrated that the known area of occurrence for Aders’ duiker has more than doubled with occupancy values at or close to 100 % for all three northern sites. An index of relative abundance for Aders’ duiker was also one to two orders of magnitude greater at these sites compared to Arabuko-Sokoke. Application of a replicate count N-mixture model to camera trap data from Boni National Reserve resulted in an estimate of 7.3 Aders’ duikers/km2 (95 % CI 4.5–10.1/km2). The results also indicate higher densities of suni Nesotragus moschatus and Harvey’s duiker Cephalophus harveyi in the northern forests relative to Arabuko-Sokoke. Blue duiker Philantomba monticola was recorded at low density in Arabuko-Sokoke forest but not detected at the northern sites. These findings significantly improve the conservation prospects for Aders’ duiker and highlight the global importance of the northern coastal forests of Kenya.

As for many tropical regions, the evolutionary and demographic status of antelope populations in the Udzungwa Mountains, Tanzania, are poorly resolved. We employed genetic information from 618 faecal samples to assess the status of forest antelope species in terms of their distribution, intraspecific diversity and population subdivision within the Udzungwa landscape. Most species were detected in the majority of forest fragments, except for Philantomba monticola. Phylogenetic analyses were consistent with traditional taxonomy with the exception of Cephalophus harveyi which was paraphyletic with respect to C. natalensis. There was strong support for three C. harveyi mtDNA clades within the Udzungwa Mountains although nuclear genetic variation did not partition strongly with these maternal lineages. Significant partitioning of genetic variation between sampling areas was detected for all species except the endangered C. spadix. Overall, our results demonstrate the value of non-invasive genetic sampling in studying the distribution and evolution of rarely observed species. As for many tropical regions, the evolutionary and demographic status of antelope populations in the Udzungwa Mountains, Tanzania, are poorly resolved. We employed genetic information from 618 faecal samples to assess the status of forest antelope species in terms of their distribution, intraspecific diversity and population subdivision within the Udzungwa landscape. Most species were detected in the majority of forest fragments, except for Philantomba monticola. Phylogenetic analyses were consistent with traditional taxonomy with the exception of Cephalophus harveyi which was paraphyletic with respect to C. natalensis. There was strong support for three C. harveyi mtDNA clades within the Udzungwa Mountains although nuclear genetic variation did not partition strongly with these maternal lineages. Significant partitioning of genetic variation between sampling areas was detected for all species except the endangered C. spadix. Overall, our results demonstrate the value of non-invasive genetic sampling in studying the distribution and evolution of rarely observed species.

Forest-dwelling antelope species are often difficult to detect during surveys due to their cryptic behaviour and densely vegetated habitats. Dung counts have traditionally been used to infer forest antelope abundance but genetic identification has shown that visual identification of ungulate dung to species is often unreliable. This study attempted to use easily obtained morphometric data from faecal pellets to statistically assign antelope dung piles to species. We measured pellets from 238 dung piles collected from the Udzungwa Mountains, south-central Tanzania, a largely forested landscape with five forest-associated antelope species including the endangered Abbott’s duiker Cephalophus spadix. The species identity of sampled dung piles was determined by amplifying a c. 600 bp fragment of the mitochondrial control region and aligning DNA sequences with published references. We found no diagnostic differences in faecal pellet size between antelope species although there were significant differences in mean pellet length and width. We employed a single variable linear discriminant analysis to predict the species of dung piles based on pellet length. Despite significant differentiation between species we obtained an overall accuracy of 58.8 % that did not meet our specified probability threshold (P

Aders’ duiker Cephalophus adersi is a small antelope endemic to the coastal forests of east Africa. Threatened by habitat loss and hunting, the species is categorized as Critically Endangered on the IUCN Red List. Until recently Aders’ duiker was known to persist only on Zanzibar, Tanzania, and in the Arabuko-Sokoke Forest National Reserve, Kenya. However, in 2004 a sighting of a single individual was reported from the Dodori forest in northern coastal Kenya, raising the possibility that the species survives elsewhere. Subsequently, an opportunistic camera-trap survey was conducted in September and October 2008 to establish the occurrence of Aders’ duiker in Kenyan coastal forests north of the Tana River. One hundred and fifty six images of Aders’ duikers were obtained from 12 of 28 camera-trap sites (46 of 358 camera-trap days), confirming the existence of a population of Aders’ duiker in the Boni–Dodori forest both inside and outside the National Reserves. In addition, we sighted individuals of the species on three occasions. The relatively high encounter rates per unit effort compared to similar data from Arabuko-Sokoke forest suggest the Boni–Dodori population is significant. Initial surveys of the local Awer community revealed that Aders’ duiker is well known by the name guno. These findings significantly improve the conservation prospects for Aders’ duiker and highlight the need for greater research and management efforts in the poorly known Boni–Dodori forest.

The ecology of many species of duiker, and other African forest antelope, is poorly known and yet knowledge of the factors determining their distribution and abundance is critical to the conservation of this increasingly threatened group. Camera-trapping was used to investigate forest antelope ecology in the biologically diverse Udzungwa Mountains, Tanzania. The relationship between cameratrapping rates and vegetation (and other habitat variables) was investigated using generalized linear modelling. Over 630 photographs of antelope were obtained, with Harvey’s duiker being the most recorded species. The camera-trap rate of Harvey’s duiker was positively related to the species diversity of small plant stems and negatively related to an index of visibility, while that of suni antelope was negatively related to the percentage ground cover of leaf-litter. The camera-trap rate of Harvey’s duiker was also negatively related to distance to the nearest village, as predicted for a species targeted for subsistence hunting. Camera-traps also recorded bushbuck and the threatened Tanzanian endemic Abbott’s duiker, but there were insufficient captures to model habitat use for these species. Results of this study illustrate the potential of camera-trapping for modelling habitat requirements and providing guidelines for the conservation management of threatened antelope populations in forest habitats.

Dung counts are frequently employed to infer abundance of antelope species in African forests, but the accuracy of dung identification has rarely been tested. We used non-invasive genetic methods to test the accuracy of both field identification and morphometrics for identifying dung samples collected in the Udzungwa Mountains, Tanzania. Species identity was established by sequencing part of the mitochondrial control region from faecal DNA. Field identification was found to be correct in only 58–76% of cases depending on the observer. Discriminant analysis of dung pellet length correctly classified 80% of samples but a larger reference sample size is needed before using this method to classify dung of unknown origin. The results of this study illustrate the potential inaccuracy of dung counts as a monitoring tool for sympatric forest antelope species when the probability of correct identification is unknown. We recommend molecular testing of species identity during forest antelope surveys before conclusions are drawn on the basis of other identification methods.

Dung-heap counts were used to estimate density of grey duiker (Sylvicapra grimmia Linnaeus 1758) in the Matobo National Park, Zimbabwe. To test assumptions of this method, defecation rate and defecation site selection were investigated under captive and field conditions, and densities were compared with independent estimates derived from territory mapping. Many assumptions were violated: males defecated more frequently than females with mean dry mass per deposit greater in females, but total daily faecal production was similar between sexes. Spatial distribution of faeces was clumped, and 52.8% of locations contained multiple deposits. Duikers exhibited habitat type preferences (i.e. low- to medium-density woodland) with herbaceous layer heights 40–100 cm and visibility >20 m. Calculated grey duiker density from dung-heap counts in cleared plots was 9.7 ± 1.3 animals km−2, approximately double the territory-mapping estimate based on Minimum Convex Polygons (5.13 animals km−2) but similar to the 75% Fixed Kernel estimate (10.95 animals km−2). Provided that sex ratios approach parity and sampled area is representative of all utilized habitats, violation of basic assumptions of the dung-heap count method has a minor effect on density estimate accuracy. Resume On a utilise les comptages de crottes pour estimer la densite de cephalophes de Grimm ((Sylvicapra grimmia Linnaeus 1758) dans le Parc National de Matobo, au Zimbabwe. Pour tester les hypotheses de cette methode, le taux de defecation et le choix du site de defecation ont eteetudies, en captivite et en liberte, et on les a compares a des estimations independantes derivees de la cartographie du territoire. De nombreuses hypotheses ont ete infirmees: les mâles defequent plus souvent que les femelles, avec une masse seche moyenne plus grande pour chaque excretion des femelles puisque la production fecale totale quotidienne est semblable pour les deux sexes. La distribution spatiale des excrements etait groupee, et 52,8% des endroits choisis contenaient de multiples depots. Les cephalophes presentaient des preferences pour certains habitats, des forets peu ou moyennement denses dont le couvert herbace se situait entre 40 et 100 cm de haut et dont la visibilite atteignait au moins 20 metres. Le calcul de la densite des cephalophes d'apres le comptage des crottes dans des endroits degages donnait 9,7 ± 1,3 animaux km−2, approximativement le double de ce que donne l'estimation basee sur la cartographie du terrain selon la methode du polygone convexe (5,13 animaux km−2), mais etait semblable aux 75% de l'estimation a noyau defini (10,95 animaux km−2). Pour autant que le sex-ratio soit proche de la parite et que l'aire ou a eu lieu l’echantillonnage soit representative de tous les habitats frequentes, cette violation des hypotheses de depart de la methode de comptage par les tas de crottes n'a qu'un effet mineur sur l'exactitude de l'estimation de la densite.

Abbott's duiker Cephalophus spadix is a forest antelope endemic to a very few high- land forests in Tanzania. Apparently extinct over much of its historical range, the species is listed as Endangered by the International Union for Conservation of Nature based on its rarity and its known current distribution in only 5 isolated upland areas: Kilimanjaro, Southern Highlands, West Usambara, Rubeho and Udzungwa Mountains. In contrast to the situation in the rest of its range, Abbott's duiker is relatively well documented and locally abundant in parts of the Udzungwa Mountains, which may now be the only stronghold for the species. We review the distribution of Abbott's duiker within the Udzungwa Mountains and present new information based on the non- invasive genetic identification of dung piles collected from the majority of forest blocks between 2006 and 2010 (73 confirmed dung samples). Our results include new records from outlying forest blocks where the presence of Abbott's duiker was previously unknown. Moreover, we present the first population-level analysis of genetic structure and diversity in this endangered species based on nuclear microsatellites and mitochondrial sequence data. While these genetic results are lim- ited due to small sample sizes, they indicate differentiation from other Abbott's duiker popula- tions, as well as low genetic diversity relative to sympatric antelope species. Finally, we discuss threats to Abbott's duiker and identify broad trends within the differently managed Udzungwa Mountain forests, and elsewhere, that suggest potentially successful conservation strategies for this neglected species.

International audience; Small to medium-sized central African forest artiodactyls constitute a diverse yet heavily hunted group composed primarily of species within the genera Cephalophus, Neotragus, Tragelaphus and Hyemoschus. Of these genera, Cephalophus is the richest with as many as seven sympatric species known to occur in central African forests. However, differentiating species from their faeces or from tissue where the whole carcass is unavailable is very difficult. In order to develop a robust molecular diagnostic for species identification, a database of mitochondrial cytochrome b (553 bp) and control region (675 bp) sequences was compiled from all forest Cephalophus species and other similarly sized, sympatric Tragelaphus, Neotragus and Hyemoschus species. Reference phylogenies from each marker were then used to recover the identity of sequences obtained from unknown faecal samples collected in the field. Results were then compared to determine which region best recovered species identity with the highest statistical support. Restriction fragment length polymorphisms (RFLPs) were also assessed as an alternative method for rapid species identification. Of themethods examined, tree-based analyses built on a geographically comprehensive database of control region sequences was the best means of reliably recovering species identity from central African duikers. However, three sister taxa appear indistinguishable (Cephalophus callipygus, Cephalophus ogilbyi and Cephalophus weynsi) and not all species were monophyletic. This lack of monophyly may be due to incomplete lineage sorting commonly observed in recently derived taxa, hybridization or the presence of nuclear translocated copies of mitochondrial DNA. The high level of intra-specific variation and lack of robust species-specific diagnostic sites made an RFLP-based approach to duiker species identification difficult to implement. The tree-based control region diagnostic presented here has many important applications including fine-scale mapping of species distributions, identification of confiscated tissue and environmental impact assessments.

Captive breeding for reintroduction is a much discussed tool in the management of endangered species. Although a number of high-profile case studies illustrate the critical role captive breeding can play in preventing species extinction (e.g., Stanley Price 1989; Kleiman & Rylands 2002; Cade & Burnham 2003), the available historical evidence indicates most reintroduction attempts failed (Griffith et al. 1989; Wolf et al. 1996). Over the past decade, the number of reintroduction programs and the body of scientific literature documenting these efforts has increased dramatically (Seddon et al. 2007), but the role of captive breeding remains controversial (e.g., Jule et al. 2008) despite well-documented successes. In its simplest form, the role of captive breeding and reintroduction in conservation is analogous to Noah’s ark. Species threatened with extinction are maintained in captivity, as if aboard an ark escaping the flood, until those factors threatening their existence are removed and they can be returned to the wild. This analogy has been widely used in the popular and scientific literature (Durrell 1976; Soule et al. 1986; Balmford et al. 1995). Here I focus on the extent to which the importance of captive breeding and reintroduction as a conservation strategy is reflected in planning and policy, particularly by the world’s zoos and aquaria. I tracked policy and opinion in the zoo and conservation biology literature and found a general decline in emphasis on captive breeding since the early 1990s until the recent recommendations for large-scale captive breeding pertaining to hundreds of species from certain taxonomic groups. It is worth considering whether these new proposals are open to the same criticisms as their predecessors and whether they

Background Anadromous migratory fish species such as Atlantic salmon (Salmo salar) have significant economic, cultural and ecological importance, but present a complex case for management and conservation due to the range of their migration. Atlantic salmon exist in rivers across the North Atlantic, returning to their river of birth with a high degree of accuracy; however, despite continuing efforts and improvements in in-river conservation, they are in steep decline across their range. Salmon from rivers across Europe migrate along similar routes, where they have, historically, been subject to commercial netting. This mixed stock exploitation has the potential to devastate weak and declining populations where they are exploited indiscriminately. Despite various tagging and marking studies, the effect of marine exploitation and the marine element of the salmon lifecycle in general, remain the "black-box" of salmon management. In a number of Pacific salmonid species and in several regions within the range of the Atlantic salmon, genetic stock identification and mixed stock analysis have been used successfully to quantify exploitation rates and identify the natal origins of fish outside their home waters - to date this has not been attempted for Atlantic salmon in the south of their European range. Results To facilitate mixed stock analysis (MSA) of Atlantic salmon, we have produced a baseline of genetic data for salmon populations originating from the largest rivers from Spain to northern Scotland, a region in which declines have been particularly marked. Using 12 microsatellites, 3,730 individual fish from 57 river catchments have been genotyped. Detailed patterns of population genetic diversity of Atlantic salmon at a sub-continent-wide level have been evaluated, demonstrating the existence of regional genetic signatures. Critically, these appear to be independent of more commonly recognised terrestrial biogeographical and political boundaries, allowing reporting regions to be defined. The implications of these results on the accuracy of MSA are evaluated and indicate that the success of MSA is not uniform across the range studied; our findings indicate large differences in the relative accuracy of stock composition estimates and MSA apportioning across the geographical range of the study, with a much higher degree of accuracy achieved when assigning and apportioning to populations in the south of the area studied. This result probably reflects the more genetically distinct nature of populations in the database from Spain, northwest France and southern England. Genetic stock identification has been undertaken and validation of the baseline microsatellite dataset with rod-and-line and estuary net fisheries of known origin has produced realistic estimates of stock composition at a regional scale. Conclusions This southern European database and supporting phylogeographic and mixed-stock analyses of net samples provide a unique tool for Atlantic salmon research and management, in both their natal rivers and the marine environment. However, the success of MSA is not uniform across the area studied, with large differences in the relative accuracy of stock composition estimates and MSA apportioning, with a much higher degree of accuracy achieved when assigning and apportioning to populations in the south of the region. More broadly, this study provides a basis for long-term salmon management across the region and confirms the value of this genetic approach for fisheries management of anadromous species.