Captive Breeding Research Articles

Global Climate Change Impacts on the Potential Distribution of Typical Trachinotus Fishes and Early Warning Assessment of Invasions

Marine habitats and ecosystems are increasingly being impacted by global climate change and the global spread of captive breeding. In this study, we focused on five typical Trachinotus species (Trachinotus anak, Trachinotus blochii, Trachinotus mookalee, Trachinotus goreenisi, Trachinotus ovatus) as research subjects. We utilized species distribution models and ecological niche models to predict the present and future potential distribution of these species, as well as to assess ecological niche overlap and evaluate the early warning of invasion by Trachinotus species. T. ovatus stands out with its broad distribution range and high adaptability to different environments. It occupies 1.114% of medium-high suitable areas, spanning 100,147 km2. Our predictions also suggest that T. ovatus would undergo a significant expansion (approximately 55% of the total area) under both past and future environmental scenarios, demonstrating a higher tolerance and adaptability to changes in ambient temperatures. It can be discerned that T. ovatus exhibits strong environmental adaptability, which may potentially lead to biological invasion along the southeastern coast of China. The T. anak, on the other hand, showed a higher expansion trend under high carbon dioxide concentrations (RCP8.5), indicating a certain convergence with carbon dioxide concentration. Our models showed that under future climatic conditions, T. ovatus would become the dominant species, with increased competition with T. mookalee and decreased competition with T. goreenisi, T. mookalee, and T. anak. Based on our findings and the net-pen culture mode of T. ovatus, we identified the hotspot habitat of T. ovatus to be located in the Indo-Pacific convergence zone. However, there is a possibility of an expansion trend towards the southeast coast of China in the future. Therefore, it is crucial to provide an early warning for the potential biological invasion of T. ovatus.

First record of captive breeding of the ornamental fish L333, King Tiger Pleco, Hypancistrus sp. (Siluriformes – Loricariidae) of the Amazon River basin

First record of captive breeding of the ornamental fish L333, King Tiger Pleco, Hypancistrus sp. (Siluriformes – Loricariidae) of the Amazon River basin

Gene flow stimulates recovery of reproductive fitness in a captive bred insect

Abstract Captive breeding can be a useful tool for the management of threatened species, but such programs often begin with a bottleneck which may lower reproductive fitness by increasing inbreeding and allowing deleterious alleles to increase in frequency by reducing effective population size. Dryococelus australis, the Lord Howe Island stick insect, is a critically endangered insect that has been bred at the Melbourne Zoo in Melbourne, Australia, since shortly after the species was rediscovered in 2001. We analysed a long‐term dataset of phenotypic measurements from this captive breeding program to determine whether reproductive fitness has declined in captivity. We found a clear signal of decline in direct (egg hatching success) and indirect (egg and nymph size) fitness indicators over time. We compared a captive line descended from the original program founders to a new hybrid line that has recent wild ancestry. The hybrid line showed an immediate improvement in egg hatch rate, suggesting the potential for genetic rescue. Egg and nymph size did not show as dramatic a change, although this line had only existed for just over a single generation at the time of data collection. These results argue strongly for the regular sourcing of new genetic material from the wild D. australis population to counteract fitness declines in captivity. Aside from benefiting the captive population, this would also improve the prospects of establishing new wild populations in the future, using individuals sourced from captivity.

Genetic diversity insights from population genomics and machine learning tools for Nordic Arctic charr (Salvelinus alpinus) populations

Arctic charr (Salvelinus alpinus) is a salmonid species of high ecological and commercial value in the Holarctic region. Nevertheless, more information is needed about its underlying genetic diversity and population structure in the Nordics, especially regarding farmed populations. High-throughput sequencing was applied in three Arctic charr populations of anadromous or landlocked origin from Finland, Norway and Sweden. More specifically, the animals from the Swedish and Norwegian populations originated from a major egg supplier and producer, respectively. Furthermore, in the case of the Finnish population, the sampled animals originated from the only active conservation program for Arctic charr in the country with a potential interest in farming. Using double-digest restriction site-associated DNA sequencing (ddRAD-seq) on more than 500 fish, over 2000 single nucleotide polymorphisms (SNPs), both in the form of individual SNPs and as read haplotypes, were used to study the genetic diversity and structure of those populations. Genetic diversity metrics were similar between the Norwegian and the Swedish populations. However, substantially lower (40–50 %) genetic diversity was found in the Finnish population. Moreover, considerable genetic differentiation was implied between the studied populations as the mean fixation index (FST) was above 0.1 in all pairwise comparisons. All populations were easily discernible through either principal component analysis (PCA) or discriminant analysis of principal components (DAPC). In addition, unsupervised machine learning models such as K-means, Gaussian and Bayesian Gaussian mixtures were assessed for their ability to detect genetic clusters. A preceding dimensionality reduction step by PCA resulted in all three models, suggesting that the most probable number of clusters was three. Overall, our study affirmed the utility of the developed ddRAD-seq genotyping method and unveiled the genetic structure of the studied populations, both of which could contribute to their more efficient management by captive breeding.

Influence of captive breeding environment on the locomotor performance and metabolism of the threatened Alcatraz Snouted Treefrog, Ololygon alcatraz

AbstractEx situ conservation is a complementary strategy to in situ efforts and is vital for safeguarding endangered species through maintenance and breeding in captivity with potential for reintroductions into natural environments. However, it is crucial to recognize that prolonged captivity can lead to diminished abilities of organisms over generations. Factors linked to the impact of phenotypic plasticity during development, such as restricted movement, may affect organism performance during ex situ conservation efforts, potentially making reintroduction into the wild unfeasible. Consequently, it is imperative to analyze physiological differences between captive‐bred and wild individuals. Therefore, this study investigates how captivity influences locomotor performance, morphology, and metabolic capacities of adults and juveniles of the threatened treefrog Ololygon alcatraz, in comparison to natural populations. We obtained proportional measurements of individuals and assessed their locomotor performance through jumping exercise. We also measured the metabolic capacities of the frogs by examining the activity of enzymes involved in energetic metabolic pathways in their skeletal muscle fibers. We found that wild adult frogs had larger limbs, greater jumping abilities, and a more glycolytic profile, while captive adult frogs had smaller limbs and increased aerobic enzyme activity compared to their wild counterparts. These differences probably arise from phenotypic plasticity in ontogenetic development that differs between captive and natural environments, as juveniles do not show such differences. These results highlight the need for innovative strategies in managing captive O. alcatraz populations, which will aid in their successful translocation to the wild and strengthen ex situ conservation efforts.

Genomic Vulnerability to Climate Change of an Australian Migratory Freshwater Fish, the Golden Perch (Macquaria ambigua).

Genomic vulnerability is a measure of how much evolutionary change is required for a population to maintain optimal genotype-environment associations under projected climates. Aquatic species, and in particular migratory ectotherms, are largely underrepresented in studies of genomic vulnerability. Such species might be well equipped for tracking suitable habitat and spreading diversity that could promote adaptation to future climates. We characterised range-wide genomic diversity and genomic vulnerability in the migratory and fisheries-important golden perch (Macquaria ambigua) from Australia's expansive Murray-Darling Basin (MDB). The MDB has a steep hydroclimatic gradient and is one of the world's most variable regions in terms of climate and streamflow. Golden perch are threatened by fragmentation and obstruction of waterways, alteration of flow regimes, and a progressively hotter and drying climate. We gathered a genomic dataset of 1049 individuals from 186 MDB localities. Despite high range-wide gene flow, golden perch in the warmer, northern catchments had higher predicted vulnerability than those in the cooler, southern catchments. A new cross-validation approach showed that these predictions were insensitive to the exclusion of individual catchments. The results raise concern for populations at warm range edges, which may already be close to their thermal limits. However, a population with functional variants beneficial for climate adaptation found in the most arid and hydrologically variable catchment was predicted to be less vulnerable. Native fish management plans, such as captive breeding and stocking, should consider spatial variation in genomic vulnerability to improve conservation outcomes under climate change, even for dispersive species with high connectivity.

Genetic Diversity and Evolutionary Biology of Indian Wildlife- A Review

The genetic diversity and evolutionary biology of Indian wildlife, emphasizing the critical role of genetic variability in ensuring species adaptability and long-term survival. India is one of the world’s megadiverse countries, home to a wide range of unique flora and fauna spread across its biodiversity hotspots, including the Western Ghats and the Eastern Himalayas. However, rapid habitat fragmentation, deforestation, and poaching have severely impacted the genetic health of many wildlife species, leading to reduced gene flow, population bottlenecks, and increased inbreeding. This has heightened the risk of extinction for small, isolated populations such as the Asiatic lion and the Great Indian bustard. Genetic studies using advanced genomic tools have provided key insights into the population structure, phylogenetic relationships, and adaptive potential of species like the Bengal tiger, Asian elephant, and snow leopard. Conservation strategies, including genetic rescue, habitat corridors, and the use of captive breeding programs, are recommended to preserve genetic diversity and prevent further genetic erosion. Technological advances, such as non-invasive sampling and bioinformatics, are transforming wildlife research, enabling more precise and less intrusive genetic monitoring. The integration of genetic data into conservation policies and practices is essential for developing targeted management plans that maintain the evolutionary potential of Indian wildlife.

Behavioral Observations of Free-Living Scarlet Macaws (Ara macao) in Costa Rica, to Inform Ex Situ Management

The scarlet macaw (Ara macao) is a charismatic species that is native to Central and South America and commonly housed in captivity. Gaps in knowledge about these birds’ behavioral ecology in the wild hinders both in situ and ex situ management and conservation efforts for this species. We conducted seventeen days of observations of free-living scarlet macaws in two locations in Costa Rica, in February 2022, with the aims of (1) advancing our knowledge of this species’ natural behavioral ecology, and (2) generating data for comparison with captive macaws to help to inform their ex situ management (e.g., enclosure design and enrichment). Routes were walked within two locations—Bosque Escondido (BE), release area for captive-bred reintroduced individuals and no extant wild population, and Punta Leona (PL), an area of natural habitat within a resort inhabited by wild scarlet macaws—and focal interval sampling of multiple scarlet macaws in a group was used to record behavior and space use. The macaws at both locations were generally active, spent most of their time high in the tree canopy, relied on climbing to move within it, and used a wide variety of supports. The macaws at PL spent significantly more time feeding and locomoting, and less time perching, than those at BE, possibly due to differences in resource availability, rearing conditions, and age. Furthermore, the wild scarlet macaws at PL exhibited a variety of foraging strategies to acquire and manipulate food items within the tree canopy, including frequent use of their feet during manipulation. Despite limitations caused by a small sample size, a short period of observations, and differences between the two populations observed, this study provides insights into the behavioral ecology of scarlet macaws in the wild, which can be used for behavioral assessments of captive macaws while informing their ex situ management, with applications to animal welfare and captive breeding programs.

Submissions of diagnostic samples of two critically endangered species of handfish (Branchionichthys hirsutus and Thymichthys politus) from a public aquarium from 2018 to 2024.

Handfish (Family Brachionichthyidae) is the most threatened marine teleost fish family, however, there is little information on handfish health. We reviewed the results of submissions of mortalities from captive and captive bred spotted handfish (Branchionichthys hirsutus (Lacepède, 1804)) and red handfish (Thymichthys politus (Richardson, 1844)) from a public aquarium from January 2018 to February 2024. Seventeen cases for spotted handfish (comprising 33 individuals) and five cases for red handfish (one individual each) were submitted for mortality investigation. In 2018-2019, six of seven cases were diagnosed with scuticociliatosis. Other conditions included epitheliocystis (1 of 17), infections with metazoan parasites (2 of 17 for spotted handfish and 2 of 5 for red handfish) and hepatic lipidosis (4 of 17). Most submissions were fixed samples for histology with only one fish suitable for microbiology. We recommend development of a coordinated health program for all captive breeders and aquaria, which should include sampling protocols, collection, and preservation in a range of fixatives of all the dying or dead handfish and adapting sublethal sampling, including tank water to assess presence of pathogens and other microorganisms. Risk factors for handfish health in captivity should be assessed. Handfish health database should be established to avoid loss of corporate knowledge in this area.

Captive Breeding Reveals Insights Into the Ecology and Reproductive Biology of 11 Little-Known Malagasy Frog Species.

Amphibians are facing an extinction crisis, with ex situ programs increasingly being used as a tool for their conservation. However, conservation efforts are often limited because we do not understand the ecological, behavioral, and life history traits of many amphibian species. Here, we report on the seasonal breeding patterns, egg-laying behavior, clutch size, and development of 11 frog species maintained at a conservation breeding facility in Andasibe, Madagascar. The frogs exhibited diverse breeding strategies aligned with life history theory. Counting the eggs in 1239 egg masses across these 11 species, we found endotrophic microhylids and terrestrial-breeding species had the smallest clutch size yet completed metamorphosis quickly, whereas species that laid eggs above or in water with exotrophic larvae had larger clutch sizes and took longer to develop. Most reproduction in captivity occurred during the warm, rainy season and followed seasonal patterns in temperature variation. Yet, Mantidactylus betsileanus bred throughout the year, and Heterixalus betsileo required additional environmental stimuli to trigger reproduction. Notably, we confirmed that Gephyromantis mitsinjo lays eggs on land with tadpoles developing terrestrially within jelly, a behavior previously theorized but which until now remained unobserved. Such observations show how captive breeding programs can be used to gain valuable data on the life history traits of species that are otherwise challenging to observe in nature. Our findings can be used to assess threats to closely related species, helping inform conservation efforts in a country harboring exceptional amphibian species richness and endemism.

Global change drives potential niche contraction and range shift of globally threatened African vulture

Human-induced global change poses an increasingly severe threat to biodiversity, with species having limited population sizes being particularly vulnerable. Mapping and modeling the distribution ranges of such species, along with detecting potential range shifts and contractions at both local and regional scales, are essential for developing effective conservation plans. Ruppell's vulture Gyps rueppelli, an ecologically important bird species native to Africa, is experiencing a rapid decline in its range. The purpose of this study is to map and model potential regional spatio-temporal distribution of Ruppell's vulture in Africa, alongside detecting the possibility of the species' range shifts and contractions. A total of 804 rarefied localities were identified where the Ruppell's vulture was the dominant bird species. This study employed the Maximum Entropy (MaxEnt) algorithm to perform species distribution modeling for the Ruppell's vulture. The modeling considered current climate conditions (1970s-2000s) as a baseline, along with two future climate change scenarios (Shared Socioeconomic Pathways: SSPs 245 and 585) for two future time periods (2050s and 2070s). The model's performance was evaluated by optimizing settings and examining the Area under the Receiver Operating Characteristic Curve (AUC-ROC). Among the 13 bioclimatic and anthropogenic variables included in the model, four (isothermality, cropland expansion, anthropogenic biomes, and urban expansion (in order of importance)) emerged as the most influential drivers of Ruppell's vulture regional distribution. All considered Species distribution models (SDMs) achieved high predictive performance, with AUC-ROC values exceeding 0.9.The model predicted a total of approximately 19,453 ha of suitable habitat for Ruppell's vultures in Africa, with East Africa identified as the most prominent region under the current climate scenario. Isothermality (38.8%) was the primary factor influencing Ruppell's vulture distribution, followed by agricultural expansion (29.9%) and anthropogenic biomes (7.2%) in the face of global change. The results reveal considerable future habitat loss (up to 61%) for Ruppell's vultures in the study area, alongside an eastward range shift (longitudinal axis) by the 2050s under projected climate change scenarios. These imply that Ruppell's vultures face imminent population decline and range shift due to significant habitat loss and climate change. Hence, prioritizing the development and implementation of a coordinated conservation program that incorporates captive breeding and assisted migration is critical to save this vulture species in its native African range.

Growth media change Eisenia fetida epithelium thickness: implications for improving earthworm welfare in vermicomposting systems.

Because the earthworm tegument represents their first barrier against environmental aggressions, we hypothesised that substrate-induced changes in earthworm growth would also alter the morphology of this protective layer. Therefore, a histological and morphometric study was performed on Eisenia fetida specimens that have been grown in five different organic residues: cow manure, horse manure, grape marc, coffee grounds, and a mixture of coffee grounds and cooking oil. The results showed that, across all treatments, both cuticle and epidermis were significantly thicker in the pre-clitellar region than after the clitellum, attributed to the fact that the former region is responsible for breaking up the soil. Notably, the growing media significantly altered the thickness of these two integumentary layers, and the greatest thicknesses were measured in grape marc and in the mixture coffee grounds + cooking oil, which makes them suitable organic residues for vermicomposting. By contrary, a significant epidermal thinning was observed when growing on coffee grounds alone, clearly indicating that it is a hostile environment for earthworms. Overall, these results reveal that tegument thickness can be used not only as a trait indicator of substrate quality but also of earthworm welfare, and it should be integrated in future toxicity assessment and captive breeding guidelines.

Seasonality in Sonoran pronghorn survival and movement within a managed rangeland

AbstractThe endangered Sonoran pronghorn (Antilocapra americana sonoriensis) has a large portion of its range within a military operations area in southwestern Arizona, USA. Sonoran pronghorn have been actively managed in this region for more than 20 years. Recovery efforts have included release of captive‐born pronghorn into areas both currently and historically occupied by wild pronghorn. These areas provide habitat for federally endangered essential and experimental non‐essential, referred to as 10(j), pronghorn populations. More than 20 years of monitoring efforts have resulted in a large dataset on their spatial occurrence and movement within these areas. To synthesize long‐term trends and seasonality in Sonoran pronghorn movement and mortality, we employed a suite of quantitative analyses that characterized the pronghorns' 1) individual and population‐level home ranges, 2) occurrence near active military targets, 3) trends in seasonal group sizes and composition, 4) sex‐ and group‐specific survivorship, and 5) changes in movement‐based behavior following release from captivity. We found strong seasonal trends throughout, including sex‐specific differences in seasonal movement rates, home ranges, survival, and group composition. Further, captive‐born pronghorn released into the endangered population exhibited markedly higher survival compared to those released in 10(j) areas. Captive‐born pronghorn exhibited significant seasonal use of active military target areas. These analyses, which represent the most comprehensive analysis of Sonoran pronghorn movement and survival to date, have important implications for the future conservation and management of this endangered species. Our results indicate that active management of endangered Sonoran pronghorn has successfully increased survival, and we recommend maintaining or increasing current recovery efforts, such as captive breeding and placement of supplemental resources throughout their range (e.g., freestanding water and supplemental forage), to further boost the survivorship of both wild‐ and captive‐born pronghorn. Moreover, future management efforts could use our seasonality results to create dynamic prediction models of when and where pronghorn are likely to overlap with military activities to best manage interactions. Our methods have added application to other mobile species of conservation interest occurring in disturbed and resource‐limited landscapes.

Identification of two effective sex-specific DNA markers in silver arowana (Osteoglossum bicirrhosum)

The silver arowana (Osteoglossum bicirrhosum), often referred to as a living fossil, presents significant challenges in sex identification based on morphological characteristics, with its sex determination mechanism remaining poorly understood. This issue poses considerable obstacles to its captive breeding efforts. Given the species' substantial value for both consumption and ornamental purposes, it is a critical candidate for aquaculture. Through genome sequencing, read mapping, and alignment analysis of five male and five female silver arowanas, along with one mixed pool of males, we successfully identified two sex-specific SNPs and confirmed a ZW model of sex determination in this ancient species. These two SNPs demonstrated remarkable accuracy, achieving 100 % success in genetic sex identification, as validated by Sanger sequencing of PCR products from 135 individuals. Both sex-specific SNPs are located approximately 26 kb upstream of the foxl2 gene, indicating a potentially pivotal role for the foxl2 gene in the sex-determination process of the silver arowana. Consequently, we have developed precise molecular markers for sex identification in the silver arowana, significantly enhancing reproductive efficiency and promoting further industrial development. This achievement lays a foundational basis for investigating the sex-determination mechanism of the silver arowana and other osteoglossid fish, thereby advancing aquaculture practices within this species.

Scorpion mud turtle breeding in the Amazon: zootechnical and environmental activity for the species conservation

Commercial captive turtle breeding is an opportunity for Kinosternon scorpioides scorpioides conservation, as predatory hunting, destruction and habitat degradation are the main threats to its natural populations. In this sense, the goal of this study is to provide a synthesis of knowledge about the species Embrapa-developed captive breeding system. Below, we have set up the themes in a way that makes sense in the captivity flow, discussing important information about the species in the environmental context and its management from the initial breeding stock formation up to reproductive aspects, highlighting animal behaviour and the environmental approach of the activity, to support commercial breeding from the species conservation perspective. The discussion and conclusions have shown that the species has a low invasive potential in Brazilian biomes; the captivity site needs not much space, facilities or water; captive breeding is a zootechnical and environmentally appropriate activity for the species’ conservation because it is a way to avoid spending on programs that are made only for this purpose; and increasing knowledge of reproduction using molecular genetic tools is important. Keywords: conservation, chelonian, Kinosternon scorpioides, jurará, turtle breeding

Embryonic development of the world's smallest puffer fish, Carinotetraodon travancoricus - a threatened freshwater fish of the Western Ghats Biodiversity Hotspot.

The Malabar dwarf puffer, Carinotetraodon travancoricus is the smallest known pufferfish (family Tetraodontidae) and one of the smallest freshwater fishes of the Indian subcontinent. Due to their miniature size, wacky behaviour and appearance, they are much preferred in the international aquarium fish trade, although little is known regarding their breeding activity in captivity and their embryonic development. The purpose of this study was to fill these knowledge gaps. Wild-caught Malabar dwarf puffers were acclimatised to conditions, and pairs were introduced to breeding tanks. Adult fishes were fed with live and frozen diets including Artemia nauplii, moina and bloodworm. During spawning seasons, adult fish displayed elaborate courtship behaviour around sunset. Carinotetraodon travancoricus is a batch spawner releasing 1 to 5 eggs per diem. The eggs were spherical, and non-sticky, with a diameter of 1.48 ± 0.1 mm, and hatching took place after 108 to 116 h post-incubation. The newly hatched larvae were 3.5 ± 0.2 mm in length, and weighed 2.9 ± 0.4 mg. The early larvae have substantial yolk and oil globules as an energy reserve. Histological studies on mature females suggested the batch spawning nature of the species and low fecundity. Given its unique reproductive behaviour and characters, in situ protected habitats are required to ensure their continued survival in the wild, apart from encouraging captive breeding to augment the demand in the international aquarium fish trade.

Can recent evolutionary history promote resilience to environmental change?

Principles of social evolution have long been used retrospectively to interpret social interactions, but have less commonly been applied predictively to inform conservation and animal husbandry strategies. We investigate whether differences in developmental environment, facilitated by divergent social conditions, can predict resilience to environmental change. Upon exposure to harsh novel environments, populations that previously experienced more benign social environments are predicted either to suffer fitness losses (the "mutation load hypothesis" and "selection filter hypothesis") or maintain fitness (the "beneficial mutation hypothesis"). We tested these contrasting predictions using populations of burying beetles Nicrophorus vespilloides we had evolved experimentally for 45 generations under contrasting social environments by manipulating the supply of post-hatching parental care. We exposed sexually immature adults from each population to varying heat stress and measured the effect on survival and reproduction. The greater the level of parental care previously experienced by a population, the better its survival under heat stress during sexual maturation. Although this is consistent with the "beneficial mutation hypothesis," it is also possible that populations that had evolved without post-hatching care were simply more prone to dying during maturation, regardless of their thermal environment. Overall, we suggest that stochastic genetic variation, probably due to founder effects, had a stronger influence on resilience. We discuss the implications for translocation and captive breeding programs.

Making Noah's Ark Work for Fishing Cat Conservation: A Blueprint for Connecting Populations across an Interactive Wild Ex Situ Spectrum.

The One Plan Approach advocates for a hybrid species management framework, wherein captive-bred populations are considered metapopulations nested within a broader network of zoos and wild populations Additionally, the Opportunities to Thrive framework aims to enhance animal welfare by addressing the physiological, psychological, and emotional needs of captive individuals, thereby improving conservation outcomes. Here, we present an integrated framework for the conservation of a globally threatened wetland wild cat species, the fishing cat, by synthesizing optimal ex situ management practices and in situ conservation strategies. Further, we examined the genetic constitution of the founder population in a fishing cat captive breeding program that was recently initiated by the West Bengal Zoo Authority, India and conducted a population viability analysis to suggest how best to maintain the genetic diversity of the population. We found that the present genetic diversity of 56% and maximum carrying capacity of the captive population (30 individuals) can be maintained for more than 100 years with a combination of supplementation and harvesting. Keeping stochastic events in mind, the introduction of two adult males and females to the existing population each year will seamlessly allow the harvesting of two adult males and two adult females every alternate year to supplement wild populations. Further, we adopted the proposed integrated framework to delineate recommendations for the supplementation of wild populations in West Bengal. We used environmental criteria known to influence fishing cat occurrence to identify 21 potential reintroduction zones in the Sundarbans landscape and Terai region in northern West Bengal with habitable areas for the fishing cat that are larger than the maximum known species' home range. Our study is timely and insightful because it provides a holistic blueprint for implementing the One Plan Approach in safeguarding a threatened species.

TigerBase: A DNA registration system to enhance enforcement and compliance testing of captive tiger facilities

The illegal trade in tigers (Panthera tigris) and their derivatives, such as bones, teeth and pelts, is a major threat to the species’ long-term persistence. As wild tiger populations have dwindled, a large proportion of trafficked tiger products now derive from captive breeding facilities found throughout Asia. Moreover, wild tigers have been poached and laundered into captive facilities, then falsely designated as captive-bred. The establishment of a DNA registration system is recognized as a key tool to monitor compliance of captive facilities, support tiger trade investigations and improve prosecution outcomes. Here, we present a standardised wildlife forensic DNA profiling system for captive tigers called TigerBase. TigerBase has been developed in four South-East Asia countries with captive tiger facilities: Malaysia, Vietnam, Thailand and Lao PDR. TigerBase DNA profile data is based on 60 single nucleotide polymorphism (SNP) markers, genotyped using two different TaqMan®-based approaches: OpenArray® chip (capable of genotyping 60 SNPs for 48 samples in a single chip), and singleplex TaqMan® assays (capable of genotyping one SNP for one sample per reaction). Of the 60 SNPs, 53 are autosomal nuclear markers, suitable for individualisation and parentage applications, two are sex-linked markers, suitable for sexing, and five are mtDNA markers, suitable for maternal subspecies identification. We conducted a series of validation experiments to investigate the reliability and limitations of these SNP genotyping platforms. We found that the OpenArray® chip platform is more appropriate for generating reference data given its greater throughput, while the singleplex TaqMan® assays are more appropriate for genotyping lower quality casework samples, given their higher sensitivity and throughput flexibility. Only 19 autosomal nuclear markers were validated as singleplex TaqMan® assays, which generally provides ample power for individualisation analysis (probability of identity among siblings was <6.9 ×10−4), but may lack power for specific parentage questions, such as determining parentage of an offspring when one of the parent’s genotypes is missing. Further, we have developed pipelines to support standardised SNP calling and decrease the chance of genotyping errors through the use of analytical workflows and synthetic positive controls. We expect the implementation of TigerBase will enhance enforcement of tiger trafficking cases and encourage compliance among captive tiger facilities, together contributing to combatting the illegal tiger trade.

Analysing the pedigree to identify undesirable losses of genetic diversity and to prioritize management decisions in captive breeding: a case study.

When prevention of species extinction is the priority, captive breeding is a key component in conservation programmes, allowing the recording of pedigree information in studbooks. The genealogical information registered in Cuvier's gazelle studbook between 1975 and 2023 was analysed to (a) assess if the implemented mating policy was successful in preserving the genetic background of the founders (1 male:3 females) in the present population, and b) improve future management and breeding decisions. Although the maternal contribution of one founder female was lost and the mean inbreeding of the total live population was high (0.305 ± 0.095), the breeding policy applied produced better results than expected from a population starting from four founders. It was successful in keeping the individual increase in inbreeding low (0.047 ± 0.021), and, notably, the inbreeding tended to decrease during the last three decades of the breeding programme, ensuring the viability of this highly inbred population. Historical dissemination of individuals among the zoos of Europe and North America caused population structuring and genetic differentiation of the live North American population. However, it did not risk the viability of the captive population. The average relatedness coefficients allowed the identification of individuals with underrepresented genotypes, which is relevant to plan future mating guidelines to keep the founders' representation balanced in the next generations. This study highlights the importance of keeping long-term pedigree information to monitor changes in the genetic diversity of captive populations, which is crucial to implement optimal mating decisions and assuring their long-term viability within an ex situ conservation programme.