Population assessment of the Endangered Kashmir Gray Langur (Semnopithecus ajax, Pocock 1928) using the double-observer method

Primates are among the most threatened taxa globally, therefore, there is a need to estimate and monitor their populations. Kashmir Gray Langur Semnopithecus ajax is an endangered species for which there is no population estimate. We used double-observer method to estimate its population size in the Kashmir region of North-Western Himalaya. We walked 1284 km across 31 survey blocks spanning all three divisions of Kashmir viz., North, Central, and South Kashmir, covering an area of 411 km2. We counted a minimum of 1367 individual langurs from 27 groups. The detection probability for observer 1 (0.719) and observer 2 (0.656) resulted in a population estimate of 1496 (95% confidence interval [CI] 1367-1899) across 30 groups (with a mean group size of 51), giving a density estimate of 3.64 (3.33-4.62) langurs/km². We found double-observer surveys to be suitable for the population estimation of langurs, and we make recommendations on how to effectively conduct primate surveys, especially in mountainous ecosystems. Our records extend the species distribution range beyond stated by the International Union for Conservation of Nature. Our findings also highlight that the Kashmir Himalaya is a stronghold of the species, where conservation efforts should focus.

Neoplasia in an assurance population of Puerto Rican crested toads (Peltophryne lemur)

Disease monitoring of amphibian assurance populations is an important buffer against ongoing global extinctions. This study documents a high incidence of neoplasia in a zoo-managed assurance population of Puerto Rican crested toads (Peltophryne lemur; PRCTs). Over 5 years, neoplasia was diagnosed in 17/49 (35%) submitted adult PRCTs and was the cause of death or euthanasia in 13/17 (72%). Most toads were male (16/17; 94%) and 6 to 11-years-old (average 8.1 years). Notably, seven toads (41%) had multiple neoplasms. Of the 29 neoplasms identified, 17 (59%) were cutaneous or subcutaneous. The most common neoplasms included mast cell tumors (MCTs; 8/29; 28%), histiocytic sarcomas (6/29; 21%), lymphoma/leukemia (4/29; 14%), and squamous cell carcinomas (3/29; 10%). Distant metastases were documented in 6/8 (75%) toads with MCTs. Causes for neoplasia in this population were not determined though may include genetic or environmental factors. Continued investigations of managed endangered amphibians will help elucidate mechanisms of carcinogenesis.

An ensemble model predicts an upward range shift of the endemic and endangered Yellow-throated Apalis (Apalis flavigularis) under future climate change in Malawi

Climate change poses a significant threat to endemic and endangered montane bird species with limited elevation and temperature ranges. Understanding their responses to changes in climate is essential for informing conservation actions. This study focused on the montane dwelling Yellow-throated Apalis (Apalis flavigularis) in Malawi, aiming to identify key factors affecting its distribution and predicting its potential distribution under different climate change scenarios. Using an ensemble species distribution modeling approach, we found that the mean temperature of the driest quarter (Bio9), mean temperature of the wettest quarter (Bio8), and precipitation seasonality (Bio15) were the most important variables that influenced the distribution of this species. Across future climate scenarios, the species' geographic range declined where range losses varied from 57.74% (2050 RCP 6.0) to 82.88% (2070 RCP 6.0). We estimate its current range size to be 549 km2 which is lower than some previous estimates of its spatial distribution. Moreover, our projections indicate that under future climate scenarios, the species will shift to higher elevations with a large proportion of suitable areas located outside forests, posing challenges for adaptation. Our results suggest that the species may be under greater threat than previously thought; hence, urgent conservation actions are required. We recommend reinforcing the protection of areas predicted to remain suitable under future climate scenarios and the development of a species conservation action plan.

The complete chloroplast genome sequence of Ammodendron bifolium (Fabaceae), an endangered desert shrub from China

Ammodendron bifolium, a rare deciduous shrub, is the only species of Ammodendron (Fabaceae) in China, which distributes in Huocheng county, Xinjiang. This study employed high-throughput sequencing technology to assemble the complete chloroplast genome sequence of A. bifolium. The entire length of chloroplast genome is 154,426 bp. It comprises 128 genes, which include 85 protein-coding genes, 35 tRNA genes, and 8 rRNA genes. The A. bifolium chloroplast genome has a GC content of 36.41%. Phylogenetic analysis strongly supported that A. bifolium is sister to the members of the Sophora genus. This study will provide the genetic information data for further phylogenetic studies of Ammodendron.

Cloning for the Twenty-First Century and Its Place in Endangered Species Conservation

Cloning as it relates to the animal kingdom generally refers to the production of genetically identical individuals. Because cloning is increasingly the subject of renewed attention as a tool for rescuing endangered or extinct species, it seems timely to dissect the role of the numerous reproductive techniques encompassed by this term in animal species conservation. Although cloning is typically associated with somatic cell nuclear transfer, the recent advent of additional techniques that allow genome replication without genetic recombination demands that the use of induced pluripotent stem cells to generate gametes or embryos, as well as older methods such as embryo splitting, all be included in this discussion. Additionally, the phenomenon of natural cloning (e.g., a subset of fish, birds, invertebrates, and reptilian species that reproduce via parthenogenesis) must also be pointed out. Beyond the biology of these techniques are practical considerations and the ethics of using cloning and associated procedures in endangered or extinct species. All of these must be examined in concert to determine whether cloning has a place in species conservation. Therefore, we synthesize progress in cloning and associated techniques and dissect the practical and ethical aspects of these methods as they pertain to endangered species conservation.

Conservation Genetics of the Endangered Lompoc Yerba Santa (Eriodictyon capitatum Eastw., Namaceae), including Phylogenomic Insights into the Evolution of Eriodictyon

Eriodictyon capitatum (Namaceae) is a narrowly distributed shrub endemic to western Santa Barbara County, where it is known from only 10 extant California Natural Diversity Database element occurrences (EOs). Owing to low numbers of plants in nature, a limited overall extent, and multiple current threats, E. capitatum is listed as Endangered under the Federal Endangered Species Act and as Rare under the California Native Plant Protection Act. In the present study, high-throughput DNA sequence data were analyzed to investigate genetic diversity within and among all accessible EOs; to determine the extent of genetic isolation among EOs; to examine clonality within EOs; and to examine the taxonomic circumscriptions of E. capitatum, E. altissimum, E. angustifolium, and E. californicum through phylogenomic analysis. Population genetic analyses of E. capitatum reveal a pattern of strong genetic differentiation by location/EO. The clonality assessment shows that certain small EOs may support relatively few multilocus genotypes. The phylogenomic analyses strongly support the present-day taxonomic circumscriptions of both E. altissimum and E. capitatum, showing them to be reciprocally monophyletic and sister with strong support. Taken together, these results paint a picture of an evolutionarily and morphologically distinct species known from relatively few, genetically isolated stations.

Gut Microbiome Profiling of the Endangered Southern Greater Glider (Petauroides volans) after the 2019-2020 Australian Megafire

Studying the gut microbiome can provide valuable insights into animal health and inform the conservation management of threatened wildlife. Gut microbiota play important roles in regulating mammalian host physiology, including digestion, energy metabolism and immunity. Dysbiosis can impair such physiological processes and compromise host health, so it is essential that the gut microbiome be considered in conservation planning. The southern greater glider (Petauroides volans) is an endangered arboreal marsupial that faced widespread habitat fragmentation and population declines following the 2019-2020 Australian bushfire season. This study details baseline data on the gut microbiome of this species. The V3-V4 region of the 16S rRNA gene was amplified from scats collected from individuals inhabiting burnt and unburnt sites across southeastern Australia and sequenced to determine bacterial community composition. Southern greater glider gut microbiomes were characterised by high relative abundances of Firmicutes and Bacteroidota, which is consistent with that reported for other marsupial herbivores. Significant differences in gut microbial diversity and community structure were detected among individuals from different geographic locations. Certain microbiota and functional orthologues were also found to be significantly differentially abundant between locations. The role of wildfire in shaping southern greater glider gut microbiomes was shown, with some significant differences in the diversity and abundance of microbiota detected between burnt and unburnt sites. Overall, this study details the first data on greater glider (Petauroides) gut microbiomes, laying the foundation for future studies to further explore relationships between microbial community structure, environmental stressors and host health.

Cloning in action: can embryo splitting, induced pluripotency and somatic cell nuclear transfer contribute to endangered species conservation?

The term 'cloning' refers to the production of genetically identical individuals but has meant different things throughout the history of science: a natural means of reproduction in bacteria, a routine procedure in horticulture, and an ever-evolving gamut of molecular technologies in vertebrates. Mammalian cloning can be achieved through embryo splitting, somatic cell nuclear transfer, and most recently, by the use of induced pluripotent stem cells. Several emerging biotechnologies also facilitate the propagation of genomes from one generation to the next whilst bypassing the conventional reproductive processes. In this review, we examine the state of the art of available cloning technologies and their progress in species other than humans and rodent models, in order to provide a critical overview of their readiness and relevance for application in endangered animal conservation.

New Strategies for Conservation of Gentile di Puglia Sheep Breed, an Autochthonous Capital of Millennial Tradition in Southern Italy

Gentile di Puglia (GdP) is an autochthonous sheep breed of Southern Italy included among ovine breeds threatened by genetic erosion and extinction risk, which have been given attention by local and international institutions, thus emphasizing the need for germplasm conservation actions. In the present study, two assisted reproduction approaches, finalized for GdP conservation, were performed: (1) on-farm reproductive efficiency evaluation, expressed as pregnancy rate (PR), twin pregnancy rate (tPR), and body condition score (BCS), for three consecutive breeding cycles and (2) pre-pubertal lambs' immature cumulus-oocyte complex (COC) retrieval, vitrification, in vitro maturation (IVM), and assessment of meiotic stage and bioenergetic-oxidative status compared with those of other Italian and European commercial breeds. PR and tPR were progressively reduced over time. In all clinical examination times, BCS was significantly lower in nonpregnant ewes compared with pregnant ones. Fresh GdP pre-pubertal lamb COCs achieved meiotic maturation and showed healthy bioenergetic-oxidative status after IVM. Vitrification reduced the oocyte maturation rate in all groups. However, mature oocytes retained their cytoplasmic maturity, expressed as a mitochondria distribution pattern and activity, indicating promising developmental competence. In conclusion, clinical- and biotechnological-assisted reproduction approaches can support conservation strategies of GdP and other local sheep breeds in Southern Italy.

Empirical Data Suggest That the Kashmir Musk Deer (Moschus cupreus, Grubb 1982) Is the One Musk Deer Distributed in the Western Himalayas: An Integration of Ecology, Genetics and Geospatial Modelling Approaches

Insufficient research has been conducted on musk deer species across their distribution range, primarily because of their elusive behaviour and the fact they occupy remote high-altitude habitats in the Himalayas above 2500 m. The available distribution records, primarily derived from ecological studies with limited photographic and indirect evidence, fail to provide comprehensive information on the species distribution. Consequently, uncertainties arise when attempting to determine the presence of specific taxonomic units of musk deer in the Western Himalayas. This lack of knowledge hampers species-oriented conservation efforts, as there need to be more species-specific initiatives focused on monitoring, protecting, and combatting the illegal poaching of musk deer for their valuable musk pods. We used transect surveys (220 trails), camera traps (255 cameras), non-invasive DNA sampling (40 samples), and geospatial modelling (279 occurrence records) to resolve the taxonomic ambiguity, and identify the suitable habitat of musk deer (Moschus spp.) in Uttarkashi District of Uttarakhand and the Lahaul-Pangi landscape of Himachal Pradesh. All the captured images and DNA-based identification results confirmed the presence of only Kashmir musk deer (KDM) (Moschus cupreus) in Uttarakhand and Himachal Pradesh. The results suggest that KMD inhabit a narrow range of suitable habitats (6.9%) of the entire Western Himalayas. Since all evidence indicates that only KMD are present in the Western Himalayas, we suggest that the presence of other species of musk deer (Alpine musk deer and Himalayan musk deer) was wrongly reported. Therefore, future conservation plans and management strategies must focus only on KMD in the Western Himalayas.

Measures of Adrenal and Gonadal Hormones in Relation to Biological and Management Factors among Captive Red Pandas in Indian Zoos

Animals in human care are affected by stressors that can ultimately reduce fitness. When reproduction is affected, endangered species conservation programs can be severely compromised. Thus, understanding factors related to stress and reproduction, and related hormones, is important to ensure captive breeding success. Red pandas (Ailurus fulgens) are endangered, and populations in the wild are threatened with extinction. A global captive breeding program has been launched to conserve the species with the goal of reintroduction. However, there is little information on how stressors impact physiological aspects of the species. This study measured fecal glucocorticoid (fGCM), progestagen (fPM), and androgen (fAM) metabolite concentrations in 12 female and 8 male red pandas at 3 zoos in India to determine predictors of adrenal and gonadal steroid activity, and the influence of fGCM on reproduction. Based on the generalized linear mixed model (GLMM), fGCM concentrations were positively correlated with the number of visitors, number of nests and enclosure areas, and negatively related to frequency of feedings, log density, and social time, while fPM concentrations were negatively associated with enclosure areas. A confounder for enclosure areas and number of nests was the fact that these spaces were relatively barren, with limited hiding spaces, compared to the smaller enclosures. By contrast, no significant relationships were found for fAM, perhaps due to the smaller sample size. A negative relationship between fGCM and fPM was observed, indicating increasing adrenal hormones may decrease reproductive function among female red pandas. Results suggest that zoo management should consider increasing feeding frequency, providing larger enclosures with more enrichment and more nests in larger spaces, and regulating visitor numbers to support good welfare and potentially improve reproductive fitness of red pandas in captivity.

Cheilolejeunea zhui (Lejeuneaceae, Marchantiophyta), a new species with moniliate ocelli from Guangxi, China

A new ocellate liverwort species, Cheilolejeunea zhui (Lejeuneaceae), is described from Guangxi, China. The new species is similar to the neotropical C. urubuensis in having moniliate ocelli in the leaf lobes and in general appearances but differs in having obliquely spreading leaves, obtuse to subacute leaf apex, thin-walled leaf cells with distinct trigones, shallowly bifid female bracteole apex, and numerous ocelli in its perianths. Molecular phylogeny of data from three regions (nrITS, trnL-F, and trnG) confirmed the systematic position of this new species to be sister to C. urubuensis, well apart from the remaining members of the genus. Based on morphological and molecular evidence, Cheilolejeunea sect. Moniliocella sect. nov. is proposed to accommodate C. urubuensis and C. zhui. The discovery of C. zhui represents the fourth known species in Cheilolejeunea with linearly arranged ocelli.

Empirical evidence for effects of invasive American Bullfrogs on occurrence of native amphibians and emerging pathogens

Invasive species and emerging infectious diseases are two of the greatest threats to biodiversity. American Bullfrogs (Rana [Lithobates] catesbeiana), which have been introduced to many parts of the world, are often linked with declines in native amphibians via predation and the spread of emerging pathogens such as amphibian chytrid fungus (Batrachochytrium dendrobatidis [Bd]) and ranaviruses. Although many studies have investigated the potential role of bullfrogs in the decline of native amphibians, analyses that account for shared habitat affinities and imperfect detection have found limited support for clear effects. Similarly, the role of bullfrogs in shaping the patch-level distribution of pathogens is unclear. We used eDNA methods to sample 233 sites in the southwestern USA and Sonora, Mexico (2016-2018) to estimate how the presence of bullfrogs affects the occurrence of four native amphibians, Bd, and ranaviruses. Based on two-species, dominant-subordinate occupancy models fitted in a Bayesian context, federally threatened Chiricahua Leopard Frogs (Rana chiricahuensis) and Western Tiger Salamanders (Ambystoma mavortium) were eight times (32% vs. 4%) and two times (36% vs. 18%), respectively, less likely to occur at sites where bullfrogs occurred. Evidence for the negative effects of bullfrogs on Lowland Leopard Frogs (Rana yavapaiensis) and Northern Leopard Frogs (Rana pipiens) was less clear, possibly because of smaller numbers of sites where these native species still occurred and because bullfrogs often occur at lower densities in streams, the primary habitat for Lowland Leopard Frogs. At the community level, Bd was most likely to occur where bullfrogs co-occurred with native amphibians, which could increase the risk to native species. Ranaviruses were estimated to occur at 33% of bullfrog-only sites, 10% of sites where bullfrogs and native amphibians co-occurred, and only 3% of sites where only native amphibians occurred. Of the 85 sites where we did not detect any of the five target amphibian species, we also did not detect Bd or ranaviruses; this suggests other hosts do not drive the distribution of these pathogens in our study area. Our results provide landscape-scale evidence that bullfrogs reduce the occurrence of native amphibians and increase the occurrence of pathogens, information that can clarify risks and aid the prioritization of conservation actions.

Skin Marks in Critically Endangered Taiwanese Humpback Dolphins (Sousa chinensis taiwanensis)

As long-lived apex predators, Indo-Pacific humpback dolphins (Sousa chinensis) are key indicators of marine coastal environmental health. Skin marks can be observed on dorsal body surfaces that are visible during mark-recapture studies that rely on photo-identification (photo-ID) methods. Skin mark prevalence may be an indicator of environmental or anthropogenic stressors in the ecosystem, which may lead to individual and/or population-level health concerns. The prevalence of marks of anthropogenic origin was assessed in the Critically Endangered S. chinensis taiwanensis population along the coasts of central Taiwan. Fifty, twenty-eight, and thirty-four individuals were identified in 2018, 2019, and 2021, respectively. At least one category of injuries was observed in 47 of 57 distinctive individuals (82%), and adults showed a higher prevalence of deep injuries than the other coloration stages. At least one category of skin lesion was observed in 33 of 57 distinctive individuals (58%), and high prevalence of skin lesions was found in mature individuals. Given the difficulty in taking direct observations, skin mark prevalence is proposed as a proxy for estimating habitat health and anthropogenic stressors upon S. chinensis taiwanensis. The moderate-to-high prevalence of skin marks in this study was designated as a warning of risks. This study provides important updated information for the assessment of the health and survival of this population. More effective management measures are urgently needed to reverse the observed population decline.

Cleft Palate Syndrome in the Endangered Spectacled Flying Fox (Pteropus conspicillatus): Implications for Conservation and Comparative Research

Cleft palate syndrome, first observed in the spectacled flying fox population in 1998, has produced sporadic neonatal mortality events over the past two decades, with an estimated incidence of up to 1/1000 births per year. This study presents a rudimentary characterisation of the syndrome, presenting gross pathology of syndromic signs upon visual inspection, a histological examination of palate malformations, and syndrome incidence data representing the past two decades. The syndrome presents with a range of signs, primarily congenital palate malformations ranging from a pinhole cleft to a complete hard and soft palate deficit, resulting in the death or abandonment of neonates shortly after birth. The congenital palate malformations are often associated with claw deformities, wiry facial hair, and in some instances, muscle weakness and neurological signs. The natural occurrence of the lethal congenital orofacial birth defects in the spectacled flying fox presents a unique opportunity for the investigation of putative aetiologies, drawing parallels between bat and other mammalian cleft palate risk factors. Further syndrome investigation has the potential to deliver both biodiversity conservation and comparative veterinary and biomedical outcomes.

Gut microbiota of endangered Australian sea lion pups is unchanged by topical ivermectin treatment for endemic hookworm infection

The gut microbiota is essential for the development and maintenance of the hosts' immune system. Disturbances to the gut microbiota in early life stages can result in long-lasting impacts on host health. This study aimed to determine if topical ivermectin treatment for endemic hookworm (Uncinaria sanguinis) infection in endangered Australian sea lion (Neophoca cinerea) pups resulted in gut microbial changes. The gut microbiota was characterised for untreated (control) (n = 23) and treated (n = 23) Australian sea lion pups sampled during the 2019 and 2020/21 breeding seasons at Seal Bay, Kangaroo Island. Samples were collected pre- and post-treatment on up to four occasions over a four-to-five-month period. The gut microbiota of untreated (control) and treated pups in both seasons was dominated by five bacterial phyla, Fusobacteria, Firmicutes, Proteobacteria, Actinobacteria and Bacteroidetes. A significant difference in alpha diversity between treatment groups was seen in pups sampled during the 2020/21 breeding season (p = 0.008), with higher richness and diversity in treated pups. Modelling the impact of individual pup identification (ID), capture, pup weight (kg), standard length (cm), age and sex on beta diversity revealed that pup ID accounted for most of the variation (35% in 2019 and 42% in 2020/21), with pup ID, capture, and age being the only significant contributors to microbial variation (p < 0.05). There were no statistically significant differences in the composition of the microbiota between treatment groups in both the 2019 and 2020/21 breeding seasons, indicating that topical ivermectin treatment did not alter the composition of the gut microbiota. To our knowledge, this is the first study to characterise the gut microbiota of free-ranging Australian pinniped pups, compare the composition across multiple time points, and to consider the impact of parasitic treatment on overall diversity and microbial composition of the gut microbiota. Importantly, the lack of compositional changes in the gut microbiota with treatment support the utility of topical ivermectin as a safe and minimally invasive management strategy to enhance pup survival in this endangered species.

iPSC Technology: An Innovative Tool for Developing Clean Meat, Livestock, and Frozen Ark

Induced pluripotent stem cell (iPSC) technology is an emerging technique to reprogram somatic cells into iPSCs that have revolutionary benefits in the fields of drug discovery, cellular therapy, and personalized medicine. However, these applications are just the tip of an iceberg. Recently, iPSC technology has been shown to be useful in not only conserving the endangered species, but also the revival of extinct species. With increasing consumer reliance on animal products, combined with an ever-growing population, there is a necessity to develop alternative approaches to conventional farming practices. One such approach involves the development of domestic farm animal iPSCs. This approach provides several benefits in the form of reduced animal death, pasture degradation, water consumption, and greenhouse gas emissions. Hence, it is essentially an environmentally-friendly alternative to conventional farming. Additionally, this approach ensures decreased zoonotic outbreaks and a constant food supply. Here, we discuss the iPSC technology in the form of a "Frozen Ark", along with its potential impact on spreading awareness of factory farming, foodborne disease, and the ecological footprint of the meat industry.

Iridoid glycosides from Picrorhiza genus endemic to the Himalayan region: phytochemistry, biosynthesis, pharmacological potential and biotechnological intercessions to boost production

Iridoid glycosides are monoterpenoids synthesized in several plant species known to exhibit a diverse range of pharmacological activities. They are used as important bioactive ingredients in many commercially available drug formulations and as lead compounds in pharmaceutical research. The genus Picrorhiza comprises two medicinally important herbs endemic to the Himalayan region viz. Picrorhiza kurrooa Royle and Picrorhiza scrophulariiflora Hong. The medicinal properties of these two species are mainly due to iridoid glycosides present in their root, rhizome, and leaves. Unregulated harvesting from the wild, habitat specificity, narrow distribution range, small population size and lack of organized cultivation led to the enrolling of these species in the endangered category by the International Union for Conservation of Nature and Natural Resources (IUCN). Therefore, there is a need for immediate biotechnological and molecular interventions. Such intercessions will open up new vistas for large-scale propagation, development of genomic/transcriptomic resources for understanding the biosynthetic pathway, the possibility of genetic/metabolic manipulations, and possible commercialization of iridoid glycosides. The current review article elucidates the phytochemistry and pharmacological importance of iridoid glycosides from the genus Picrorhiza. In addition, the role of biotechnological approaches and opportunities offered by next-generation sequencing technologies in overcoming challenges associated with the genetic engineering of these species are also discussed.

The Complete Genome Sequence of Cyanopsitta spixii, the Spix's Macaw

The Spix's Macaw (Cyanopsitta spixii) is a critically endangered parrot that was once endemic to Brazil. We present the whole genome sequence of this species. Illumina sequencing was performed on a genetic sample from a single captive individual. The reads were assembled using a de novo method followed by a series of references from related species for finishing. The raw and assembled data is publicly available via Genbank: Sequence Read Archive (SRR15037507) and Assembly (GCA_024336845).

Status and distribution of jaguarundi in Texas and Northeastern México: Making the case for extirpation and initiation of recovery in the United States

The jaguarundi (Puma yagouaroundi) is a small felid with a historical range from central Argentina through southern Texas. Information on the current distribution of this reclusive species is needed to inform recovery strategies in the United States where its last record was in 1986 in Texas. From 2003 to 2021, we conducted camera‐trap surveys across southern Texas and northern Tamaulipas, México to survey for medium‐sized wild cats (i.e., ocelots [Leopardus pardalis], bobcats [Lynx rufus], and jaguarundi). After 350,366 trap nights at 685 camera sites, we did not detect jaguarundis at 16 properties or along 2 highways (1050 km²) in Texas. However, we recorded 126 jaguarundi photographic detections in 15,784 trap nights on 2 properties (125.3 km²) in the northern Sierra of Tamaulipas, Tamaulipas, México. On these properties, latency to detection was 72 trap nights, with a 0.05 probability of detection per day and 0.73 photographic event rate every 100 trap nights. Due to a lack of confirmed class I sightings (e.g., specimen, photograph) in the 18 years of this study, and no other class I observations since 1986 in the United States, we conclude that the jaguarundi is likely extirpated from the United States. Based on survey effort and results from México, we would have expected to detect jaguarundis over the course of the study if still extant in Texas. We recommend that state and federal agencies consider jaguarundis as extirpated from the United States and initiate recovery actions as mandated in the federal jaguarundi recovery plan. These recovery actions include identification of suitable habitat in Texas, identification of robust populations in México, and re‐introduction of the jaguarundi to Texas.

Threatened Species Initiative: Empowering conservation action using genomic resources

Globally, 15,521 animal species are listed as threatened by the International Union for the Conservation of Nature, and of these less than 3% have genomic resources that can inform conservation management. To combat this, global genome initiatives are developing genomic resources, yet production of a reference genome alone does not conserve a species. The reference genome allows us to develop a suite of tools to understand both genome-wide and functional diversity within and between species. Conservation practitioners can use these tools to inform their decision-making. But, at present there is an implementation gap between the release of genome information and the use of genomic data in applied conservation by conservation practitioners. In May 2020, we launched the Threatened Species Initiative and brought a consortium of genome biologists, population biologists, bioinformaticians, population geneticists, and ecologists together with conservation agencies across Australia, including government, zoos, and nongovernment organizations. Our objective is to create a foundation of genomic data to advance our understanding of key Australian threatened species, and ultimately empower conservation practitioners to access and apply genomic data to their decision-making processes through a web-based portal. Currently, we are developing genomic resources for 61 threatened species from a range of taxa, across Australia, with more than 130 collaborators from government, academia, and conservation organizations. Developed in direct consultation with government threatened-species managers and other conservation practitioners, herein we present our framework for meeting their needs and our systematic approach to integrating genomics into threatened species recovery.

First natural breeding of the endangered dusky gopher frog (Lithobates sevosus) in captivity

To date, all captive breeding of the dusky gopher frog, Lithobates sevosus, a federally listed endangered species, has been accomplished using in vitro fertilization (IVF). Here, we describe multievent and highly fecund captive reproduction of dusky gopher frogs driven solely by natural environmental factors. Six pairs of L. sevosus were kept in a 3.7 × 4.4 m² outdoor enclosure designed to resemble their natural breeding habitat, which included a pool and three artificial burrows. Modifications to the enclosure that simulated temperatures and conditions within their natural range during winter were added in October and removed in late February. Following a warm, rainy period, five egg masses were laid between March 5 and 11, 2020. The number of oocytes per egg mass was 2300 ± 409 (range = 1341–3565), with the total across all five egg masses being 11,501. Of these oocytes, the hatching rate was 68.58 ± 10.05% (range = 37.53%–95.59%), with a total of 7887 successful hatchlings overall. Clutch sizes were similar to those in the wild and greater than those typically produced using IVF; thus, natural breeding can substantially increase the number of frogs available for reintroduction programs. Although assisted reproductive technologies such as IVF will continue to be useful for ensuring the success of strategic genetic pairings of captive L. sevosus, the new tool of nonassisted reproduction in specifically designed outdoor enclosures is an important advancement for the conservation and recovery of this endangered species.

The first captive breeding of the dusky gopher frog, Lithobates sevosus, triggered by environmental factors rather than assisted laboratory technologies is reported. Natural breeding increased recruitment into captive and in situ populations.

Development of a Sperm Cryopreservation Protocol for Critically Endangered Mohashol, Tor tor (Hamilton)

This study dealt with the development of a sperm cryopreservation protocol of Tor tor. Sperm was collected from hormone-induced males and the concentration and pH of sperm were estimated as 4.3 ± 0.1 × 10¹⁰ cells/mL and 8.6 ± 0.2, respectively. Activation of sperm motility was evaluated in different osmolalities of NaCl solution where motility of sperm decreased with increasing osmolality of extenders, and was completely inhibited at 319 mOsmol/kg. Similarly, the swimming duration of activated sperm was affected as the osmolality of the extender increased. The duration of initial motility of sperm was recorded as 8.4 ± 0.4 minutes at 48 mOsmol/kg, while the highest motility was recorded as 68.0 ± 7.2 minutes at 128 mOsmol/kg. To evaluate the toxicity of cryoprotectants, sperm was incubated with dimethyl sulfoxide (DMSO) and methanol at 5%, 10%, and 15% concentrations, respectively, for 5-45 minutes. Alsever's solution with 5% and 10% DMSO produced better motility during 5-10 minutes of incubation and 15% DMSO seemed toxic to sperm. For the cryopreservation of sperm, Alsever's solution, egg yolk citrate, and urea egg yolk were used as extenders with DMSO and methanol. Alsever's solution with 10% DMSO provided the highest equilibration (90.0% ± 3.5%) and post-thaw (80.0% ± 3.5%) motility followed by that of 87.0% ± 2.0% and 79.0% ± 1.9% with egg yolk citrate plus DMSO, and 82.0% ± 2.6% and 78.0% ± 2.0% with urea egg yolk plus DMSO, respectively. The sperm cryopreservation protocol developed through this study can be applied for long-term preservation of genetic materials of the critically endangered T. tor, and eventually, it will be an effective tool for protecting them from extinction.

An Introduction to the Callithrix Genus and Overview of Recent Advances in Marmoset Research

We provide here a current overview of marmoset (Callithrix) evolution, hybridization, species biology, basic/biomedical research, and conservation initiatives. Composed of 2 subgroups, the aurita group (C aurita and C flaviceps) and the jacchus group (C geoffroyi, C jacchus, C kuhlii, and C penicillata), this relatively young primate radiation is endemic to the Brazilian Cerrado, Caatinga, and Atlantic Forest biomes. Significant impacts on Callithrix within these biomes resulting from anthropogenic activity include (1) population declines, particularly for the aurita group; (2) widespread geographic displacement, biological invasions, and range expansions of C jacchus and C penicillata; (3) anthropogenic hybridization; and (4) epizootic Yellow Fever and Zika viral outbreaks. A number of Brazilian legal and conservation initiatives are now in place to protect the threatened aurita group and increase research about them. Due to their small size and rapid life history, marmosets are prized biomedical models. As a result, there are increasingly sophisticated genomic Callithrix resources available and burgeoning marmoset functional, immuno-, and epigenomic research. In both the laboratory and the wild, marmosets have given us insight into cognition, social group dynamics, human disease, and pregnancy. Callithrix jacchus and C penicillata are emerging neotropical primate models for arbovirus disease, including Dengue and Zika. Wild marmoset populations are helping us understand sylvatic transmission and human spillover of Zika and Yellow Fever viruses. All of these factors are positioning marmosets as preeminent models to facilitate understanding of facets of evolution, hybridization, conservation, human disease, and emerging infectious diseases.

Genome Sequence of Elaeagnus mollis, the First Chromosome-Level Genome of the Family Elaeagnaceae

Elaeagnus mollis Diels (Elaeagnaceae) is a species of shrubs and/or dwarf trees that produces highly nutritious nuts with abundant oil and pharmaceutical properties. It is endemic to China but endangered. Therefore, to facilitate the protection of its genetic resources and the development of its commercially attractive traits we generated a high-quality genome of E. mollis. The contig version of the genome (630.96 Mb long) was assembled into 14 chromosomes using Hi-C data, with contig and scaffold N50 values of 18.40 and 38.86 Mb, respectively. Further analyses identified 397.49 Mb (63.0%) of repetitive sequences and 27,130 protein-coding genes, of which 26,725 (98.5%) were functionally annotated. Benchmarking Universal Single-Copy Ortholog assessment indicated that 98.0% of highly conserved plant genes are completely present in the genome. This is the first reference genome for any species of Elaeagnaceae and should greatly facilitate future efforts to conserve, utilize, and elucidate the evolution of this endangered endemic species.

Molecular Detection and Characterization of Intestinal and Blood Parasites in Wild Chimpanzees (Pan troglodytes verus) in Senegal

Simple Summary

Western chimpanzees are currently listed as a Critically Endangered subspecies. Human encroachment has taken a toll on this great ape due to fragmented habitat and the exchange of pathogens. This epidemiological study investigated the occurrence and genetic diversity of intestinal and blood parasites in faecal samples from wild chimpanzees living in the Dindefelo Community Nature Reserve, Senegal. We paid special attention to potential human-driven sources of infection and transmission pathways. Potential diarrhoea-causing protist parasites (e.g., Cryptosporidium spp., Giardia duodenalis, Entamoeba histolytica) were detected at low infection rates (and densities) or absent, whereas commensals (Entamoeba dispar) or protist of uncertain pathogenicity (Blastocystis sp.) were far more abundant. We detected Sarcocystis spp. in chimpanzee faeces. Blood protist parasites such as Plasmodium spp. and Trypanosoma brucei spp. (the etiological agents of malaria and sleeping sickness, respectively, in humans) were also found at low prevalences, but microfilariae of the nematode Mansonella perstans were frequently found. Molecular analyses primarily revealed host-adapted species/genotypes and an apparent absence of gastrointestinal clinical manifestations in infected chimpanzees. Zoonotic events of still unknown frequency and directionality may have taken part between wild chimpanzees and humans sharing natural habitats and resources.

Abstract

Wild chimpanzee populations in West Africa (Pan troglodytes verus) have dramatically decreased as a direct consequence of anthropogenic activities and infectious diseases. Little information is currently available on the epidemiology, pathogenic significance, and zoonotic potential of protist species in wild chimpanzees. This study investigates the occurrence and genetic diversity of intestinal and blood protists as well as filariae in faecal samples (n = 234) from wild chimpanzees in the Dindefelo Community Nature Reserve, Senegal. PCR-based results revealed the presence of intestinal potential pathogens (Sarcocystis spp.: 11.5%; Giardia duodenalis: 2.1%; Cryptosporidium hominis: 0.9%), protist of uncertain pathogenicity (Blastocystis sp.: 5.6%), and commensal species (Entamoeba dispar: 18.4%; Troglodytella abrassarti: 5.6%). Entamoeba histolytica, Enterocytozoon bieneusi, and Balantioides coli were undetected. Blood protists including Plasmodium malariae (0.4%), Trypanosoma brucei (1.3%), and Mansonella perstans (9.8%) were also identified. Sanger sequencing analyses revealed host-adapted genetic variants within Blastocystis, but other parasitic pathogens (C. hominis, P. malariae, T. brucei, M. perstans) have zoonotic potential, suggesting that cross-species transmission between wild chimpanzees and humans is possible in areas where both species overlap. Additionally, we explored potential interactions between intestinal/blood protist species and seasonality and climate variables. Chimpanzees seem to play a more complex role on the epidemiology of pathogenic and commensal protist and nematode species than initially anticipated.

Automated detection of frog calls and choruses by pulse repetition rate

Anurans (frogs and toads) are among the most globally threatened taxonomic groups. Successful conservation of anurans will rely on improved data on the status and changes in local populations, particularly for rare and threatened species. Automated sensors, such as acoustic recorders, have the potential to provide such data by massively increasing the spatial and temporal scale of population sampling efforts. Analyzing such data sets will require robust and efficient tools that can automatically identify the presence of a species in audio recordings. Like bats and birds, many anuran species produce distinct vocalizations that can be captured by autonomous acoustic recorders and represent excellent candidates for automated recognition. However, in contrast to birds and bats, effective automated acoustic recognition tools for anurans are not yet widely available. An effective automated call-recognition method for anurans must be robust to the challenges of real-world field data and should not require extensive labeled data sets. We devised a vocalization identification tool that classifies anuran vocalizations in audio recordings based on their periodic structure: the repeat interval-based bioacoustic identification tool (RIBBIT). We applied RIBBIT to field recordings to study the boreal chorus frog (Pseudacris maculata) of temperate North American grasslands and the critically endangered variable harlequin frog (Atelopus varius) of tropical Central American rainforests. The tool accurately identified boreal chorus frogs, even when they vocalized in heavily overlapping choruses and identified variable harlequin frog vocalizations at a field site where it had been very rarely encountered in visual surveys. Using a few simple parameters, RIBBIT can detect any vocalization with a periodic structure, including those of many anurans, insects, birds, and mammals. We provide open-source implementations of RIBBIT in Python and R to support its use for other taxa and communities.

The effects of captivity on the microbiome of the endangered Comal Springs riffle beetle (Heterelmis comalensis)

The gut microbiome is affected by host intrinsic factors, diet and environment, and strongly linked to host's health. Although fluctuations of microbiome composition are normal, some are due to changes in host environmental conditions. When species are moved into captive environments for conservation, education or rehabilitation, these new conditions can influence a change in gut microbiome composition. Here, we compared the microbiomes of wild and captive Comal Springs riffle beetles (Heterelmis comalensis) by using amplicon sequencing of the 16S rRNA gene. We found that the microbiome of captive beetles was more diverse than wild beetle microbiomes. We identified 24 amplicon sequence variants (ASVs) with relative abundances significantly different between the wild and captive beetles. Many of the ASVs overrepresented in captive beetle microbiomes belong to taxa linked to nitrogen-rich environments. This is one of the first studies comparing the effects of captivity on the microbiome of an endangered insect species. Our findings provide valuable information for future applications in the management of captive populations of H. comalensis.

What Are the Keys to the Adaptive Success of European Wild Rabbit (Oryctolagus cuniculus) in the Iberian Peninsula?

The European wild rabbit (Oryctolagus cuniculus) plays an important ecological role in the ecosystems of the Iberian Peninsula. Recently, rabbit populations have drastically reduced, so the species is now considered endangered. However, in some places, this animal is considered a pest. This is the conservation paradox of the 21st century: the wild rabbit is both an invasive alien and an endangered native species. The authors of this review aimed to understand the keys to the adaptive success of European rabbits, addressing all aspects of their biology in order to provide the keys to the ecological management of this species. Aspects including nutrition, genetics, immunity interactions with the environment, behaviour, and conflict with human activities were reviewed. Ultimately, rabbits are resilient and adaptable. The main adaptations that explain the rabbit's adaptive success are its nutrition (wide adaptation to food and good nutritional use of caecotrophy), immune system (powerful and developed), and other aspects related to genetics and behaviour. Rabbits' relationship with humans has led them to colonise other places where they have become pests. Despite these adaptations, populations in native places have been drastically reduced in recent years. Since it serves as a bastion of the Mediterranean ecosystem, a specific conservation program for this species must be carried out. Therefore, a study of the rabbit's response to diseases and nutrition (especially protein), as well as the interaction between them, is of special interest.

Immunogenicity of Newcastle Disease Vaccine in Southern Ground-hornbill (Bucorvus leadbeateri)

The southern ground-hornbill (Bucorvus leadbeateri; hereafter SGH) is endangered in South Africa, Namibia, and Swaziland. Through a conservation program established in South Africa by the Mabula Ground Hornbill Project, wild populations are being re-established by the reintroduction of captive-reared birds. The SGH is susceptible to infection with avian avulavirus 1, which causes Newcastle disease (ND). Four different vaccines to protect against ND were administered through various vaccination schedules and evaluated by serologic monitoring to assess the efficiency and safety of various combinations of vaccines (live versus inactivated/killed), vaccine strains (Ulster strain, live; Avivac Cellimune, live; VG/GA strain, live; and Avivac Struvac, killed), and administration routes (intraocular versus subcutaneous versus intramuscular injection versus oral). We vaccinated 75 individuals and evaluated antibody titers in 53 individuals (24 juveniles, 13 subadults, and 16 adult SGH; 26 males and 27 females) over a period of 9 years. Antibody titers to avian avulavirus 1 in sera were monitored by a hemagglutination inhibition test. Protective titers were generated with 3/6 vaccine regimes tested in the SGH. The highest vaccine titers were established in birds vaccinated with the Ulster strain in the conjunctiva and followed with an intramuscular Struvac injection (mean log₂ titer 8.6 ± 2.6) booster. Our aim was 1) to assess whether optimal vaccination protocols could be developed and 2) to then be able, by oral administration, to remove the need to recapture free-roaming, reintroduced birds to administer the initial vaccine or booster, thus remove the threat or mortality associated with ND to this endangered avian species in both captive birds and birds released back into the wild.

The mitochondrial genome of the endangered Spiny Butterfly Ray Gymnura altavela (Linnaeus 1758) (Myliobatiformes: Gymnuridae) provides insights into cryptic lineages

The Spiny Butterfly Ray, Gymnura altavela, is found in tropical and temperate coastal waters with a discontinuous distribution: it occurs along the east coast of the United States of America, Brazil, and Uruguay in the western Atlantic Ocean, from Portugal to Angola in the eastern Atlantic, and also in the Mediterranean Sea. Globally, Gymnura altavela is considered endangered by the International Union for Conservation of Nature (IUCN). Our study analyzed the complete mitochondrial genome of G. altavela sequenced from an individual captured in the western Atlantic and compared it with a mitochondrial genome from a conspecific collected in the Mediterranean to explore if G. altavela comprises cryptic species. The newly assembled mitochondrial genome of G. altavela is 19,361bp in length and has 13 protein-coding genes (PCGs), two ribosomal RNA genes (12s ribosomal RNA and 16s ribosomal RNA), 22 transfer RNA (tRNA) genes, and a 3,659 bp control region. The gene order is identical to that reported for the specimen collected in the Mediterranean and that of the congeneric Long-tailed Butterfly Ray, G. poecilura. A phylomitogenomic analysis based on translated PCGs supported the monophyly of the genus Gymnura and indicated that genetic dissimilarity between G. altavela from the western Atlantic Ocean and the Mediterranean Sea was greater than that calculated among congeneric species belonging to the genera Mobula and Neotrygon, similar to that calculated among congeneric stingrays in the genus Hemitrygon, but lower than that calculated among congeneric species in the genera Pateobatis and Urogymnus. Overall, our comparisons suggest that G. altavela comprises cryptic species or at least indicates considerable genetic structure between populations in the western Atlantic and Mediterranean. We present these findings in a phylomitogenomic analysis of other Myliobatiformes and Rhinopristiformes. Additional phylogeographic and taxonomic studies of G. altavela are needed to support conservation efforts for this endangered ray that may comprise cryptic evolutionary units.

Genomic Characterisation of a Novel Avipoxvirus Isolated from an Endangered Northern Royal Albatross (Diomedea sanfordi)

Marine bird populations have been declining globally with the factors driving this decline not fully understood. Viral diseases, including those caused by poxviruses, are a concern for endangered seabird species. In this study we have characterised a novel avipoxvirus, tentatively designated albatrosspox virus (ALPV), isolated from a skin lesion of an endangered New Zealand northern royal albatross (Diomedea sanfordi). The ALPV genome was 351.9 kbp in length and contained 336 predicted genes, seven of which were determined to be unique. The highest number of genes (313) in the ALPV genome were homologs of those in shearwaterpox virus 2 (SWPV2), while a further 10 were homologs to canarypox virus (CNPV) and an additional six to shearwaterpox virus 1 (SWPV1). Phylogenetic analyses positioned the ALPV genome within a distinct subclade comprising recently isolated avipoxvirus genome sequences from shearwater, penguin and passerine bird species. This is the first reported genome sequence of ALPV from a northern royal albatross and will help to track the evolution of avipoxvirus infections in this endangered species.

(Caryophyllaceae)

The genus Silene L. is one of the largest genera in Caryophyllaceae, and is distributed in the Northern Hemisphere and South America. The endemic species Silene leucophylla and the near-endemic S. schimperiana are native to the Sinai Peninsula, Egypt. They have reduced population size and are endangered on national and international scales. These two species have typically been disregarded in most studies of the genus Silene. This research integrates the Scanning Electron Microscope (SEM), species micromorphology, and the phylogenetic analysis of four DNA markers: ITS, matK, rbcL and psb-A/trn-H. Trichomes were observed on the stem of Silene leucophylla, while the S. schimperiana has a glabrous stem. Irregular epicuticle platelets with sinuate margin were found in S. schimperiana. Oblong, bone-shaped, and irregularly arranged epidermal cells were present on the leaf of S. leucophylla, while Silene schimperiana leaf has "tetra-, penta-, hexa-, and polygonal" epidermal cells. Silene leucophylla and S. schimperiana have amphistomatic stomata. The Bayesian phylogenetic analysis of each marker individually or in combination represented the first phylogenetic study to reveal the generic and sectional classification of S. leucophylla and S. schimperiana. Two Silene complexes are proposed based on morphological and phylogenetic data. The Leucophylla complex was allied to section Siphonomorpha and the Schimperiana complex was related to section Sclerocalycinae. However, these two complexes need further investigation and more exhaustive sampling to infer their complex phylogenetic relationships.

Selection and introgression facilitated the adaptation of Chinese native endangered cattle in extreme environments

Although persistent efforts have identified and characterized a few candidate genes and related biological processes with potential functions in the adaptation of many species to extreme environments, few works have been conducted to determine the genomic basis of adaptation in endangered livestock breeds that have been living in extreme conditions for more than thousands of years. To fill this gap, we sequenced the whole genomes of nine individuals from three Chinese native endangered cattle breeds that are living in high-altitude or arid environments. Phylogenetic and evolutionary history analyses of these three and other six breeds showed that the genetic structure of the cattle populations is primarily related to geographic location. Interestingly, we identified pervasive introgression from the yak to Zhangmu cattle (ZMC) that cover several genes (e.g., NOS2, EGLN1 and EPAS1) involved in the hypoxia response and previously identified as positive selection genes in other species, which suggested that the adaptive introgression from yak may have contributed to the adaptation of ZMC to high-altitude environments. In addition, by contrasting the breeds in opposite living conditions, we revealed a set of candidate genes with various functions from hypoxia response, water metabolism, immune response and body shape change to embryo development and skeletal system development, etc., that may be related to high-altitude or arid adaptation. Our research provides new insights into the recovery and adaptation of endangered native cattle and other species in extreme environments and valuable resources for future research on animal husbandry to cope with climate change.

The complete chloroplast genome sequence of Ficus beipeiensis (Moraceae), an endemic and endangered plant in China

Ficus beipeiensis S.S.Chang is an evergreen plant of Ficus from the family Moraceae. This is an endangered species endemic to China. In terms of economic value, F. beipeiensis are used as a native plant resource of urban landscaping in Chongqing, China. Here, we sequenced, assembled and annotated the chloroplast (cp) genome of F. beipeiensis, and aim to provide genetic resources for this endangered species. The length of cp genome was 160,595 bp, with a large single-copy region (LSC) of 88,683 bp and a small single-copy region (SSC) of 20,160 bp separated by a pair of inverted repeats (IRs) of 25,876 bp. It encodes 110 unique genes, including 76 protein-coding genes, 30 transfer RNA genes, and 4 ribosomal RNA genes. Besides, we reconstructed the phylogeny of Moraceae based on the whole cp genome sequences data set. Phylogenetic analysis shows that all analyzed Ficus species are clustered and form a monophyletic group. Antiaris is a sister group to Ficus. In our maximum likelihood (ML) tree, F. beipeiensis is closely related to F. racemose.

Why Variation in Flower Color May Help Reproductive Success in the Endangered Australian Orchid Caladenia fulva

Caladenia fulva G.W. Carr (Tawny Spider-orchid) is a terrestrial Australian endangered orchid confined to contiguous reserves in open woodland in Victoria, Australia. Natural recruitment is poor and no confirmed pollinator has been observed in the last 30 years. Polymorphic variation in flower color complicates plans for artificial pollination, seed collection and ex situ propagation for augmentation or re-introduction. DNA sequencing showed that there was no distinction among color variants in the nuclear ribosomal internal transcribed spacer (ITS) region and the chloroplast trnT-trnF and matK regions. Also, authentic specimens of both C. fulva and Caladenia reticulata from the reserves clustered along with these variants, suggesting free interbreeding. Artificial cross-pollination in situ and assessment of seed viability further suggested that no fertility barriers existed among color variants. Natural fruit set was 15% of the population and was proportional to numbers of the different flower colors but varied with orchid patch within the population. Color modeling on spectral data suggested that a hymenopteran pollinator could discriminate visually among color variants. The similarity in fruiting success, however, suggests that flower color polymorphism may avoid pollinator habituation to specific non-rewarding flower colors. The retention of large brightly colored flowers suggests that C. fulva has maintained attractiveness to foraging insects rather than evolving to match a scarce unreliable hymenopteran sexual pollinator. These results suggest that C. fulva should be recognized as encompassing plants with these multiple flower colors, and artificial pollination should use all variants to conserve the biodiversity of the extant population.

Reliable eDNA detection and quantification of the European weather loach (Misgurnus fossilis)

The European weather loach (Misgurnus fossilis) is a cryptic and poorly known fish species of high conservation concern. The species is experiencing dramatic population collapses across its native range to the point of regional extinction. Although environmental DNA (eDNA)-based approaches offer clear advantages over conventional field methods for monitoring rare and endangered species, accurate detection and quantification remain difficult and quality assessment is often poorly incorporated. In this study, we developed and validated a novel digital droplet PCR (ddPCR) eDNA-based method for reliable detection and quantification, which allows accurate monitoring of M. fossilis across a number of habitat types. A dilution experiment under laboratory conditions allowed the definition of the limit of detection (LOD) and the limit of quantification (LOQ), which were set at concentrations of 0.07 and 0.14 copies μl^-1 , respectively. A series of aquarium experiments revealed a significant and positive relationship between the number of individuals and the eDNA concentration measured. During a 3 year survey (2017-2019), we assessed 96 locations for the presence of M. fossilis in Flanders (Belgium). eDNA analyses on these samples highlighted 45% positive detections of the species. On the basis of the eDNA concentration per litre of water, only 12 sites appeared to harbour relatively dense populations. The other 31 sites gave a relatively weak positive signal that was typically situated below the LOQ. Combining sample-specific estimates of effective DNA quantity (Q_e ) and conventional field sampling, we concluded that each of these weak positive sites still likely harboured the species and therefore they do not represent false positives. Further, only seven of the classified negative samples warrant additional sampling as our analyses identified a substantial risk of false-negative detections (i.e., type II errors) at these locations. Finally, we illustrated that ddPCR outcompetes conventional qPCR analyses, especially when target DNA concentrations are critically low, which could be attributed to a reduced sensitivity of ddPCR to inhibition effects, higher sample concentrations being accommodated and higher sensitivity obtained.

Euphorbiambuinzauensis, a new succulent species in Kenya from the Synadenium group in Euphorbiasect.Monadenium (Euphorbiaceae)

Euphorbiambuinzauensis, a succulent new species of the Synadenium group in Euphorbiaceae from Makueni County, Kenya, is described and illustrated. Morphologically, it is most similar to E.pseudomollis, but differs mainly by its shrubby habit (up to 4 m), abaxial leaves surfaces with densely stellate hairs, 2-4-forked cymes, smaller bracts (ca. 2.5 × 3.0 mm), smaller cyathia (6 mm wide), crimson glands without narrow smooth margin, smaller fruits (ca. 8 × 7 mm) and ovoid seeds (ca. 1.8 × 2.2 mm). Furthermore, we performed a molecular phylogenetic analysis of the Synadenium group in Euphorbiasect.Monadenium, based on complete nuclear ribosomal DNA (nrDNA) datasets. This phylogenetic inference also supports it to be a distinct species. The new species is assessed as Endangered using the IUCN criteria.

Enhancing Conservation of a Globally Imperiled Rockland Herb (Linum arenicola) through Assessments of Seed Functional Traits and Multi-Dimensional Germination Niche Breadths

Humans currently face an extraordinary period of plant biodiversity loss. One strategy to stem further losses involves the development of species-level recovery plans that guide conservation actions. Seeds represent an important component in the life history of plants and are crucial for conservation activities. Yet, most recovery plans contain meager seed biology information. We set out to examine seed functional traits and germination niche breadth of Linum arenicola seeds exposed to a range of thermal, photoperiodic, and salinity gradients to gain perspectives on the seed biology of this endangered species that may inform conservation decision making and assist recovery plan development. We found that fresh seeds possess non-deep physiological dormancy, which may be alleviated via a four-week dry after-ripening treatment. The germination response of non-dormant seeds is subsequently promoted by constant rather than alternating temperatures. The optimum germination temperature range is 20–22 °C. Non-dormant seeds do not possess an absolute light requirement for germination, but are sensitive to low levels of salinity (EC₅₀ = 6.34 ppth NaCl). The narrow thermal and salinity germination niche breadths reported here suggest a specialized reproductive strategy that may require careful consideration when planning ex and in situ conservation activities.

A new species of the genus Acanthosaura (Squamata, Agamidae) from Yunnan, China, with comments on its conservation status

A new species of Acanthosaura from Yunnan, China, is described based on morphological and genetic data. The new species can be separated from all other species of the genus by having a different shape of the black eye patch, a different coloration of the postorbital and occipital spines and nuchal crest, and a different color of the gular pouch. Genetically, uncorrected sequence divergences of COI between the new species and investigated congeners ranged from 16.12% to 24.11%. The conservation status of the new species is also discussed.

Seasonal variation in thermal tolerance of redside dace Clinostomus elongatus

Organisms living in environments with oscillating temperatures may rely on plastic traits to sustain thermal tolerance during high temperature periods. Phenotypic plasticity in critical thermal maximum (CTmax) is a powerful thermoregulative strategy that enables organisms to adjust CTmax when ambient temperatures do not match thermal preference. Given that global temperatures are increasing at an unprecedented rate, identifying factors that affect the plastic response in CTmax can help predict how organisms are likely to respond to changes in their thermal landscape. Using an experimental thermal chamber in the field, we investigated the effect of short-term acclimation on the CTmax and thermal safety margin (TSM) of wild-caught redside dace, Clinostomus elongatus, (n = 197) in a northern population in Two Tree River, Ontario. Streamside CTmax trials were used to identify the maximum temperature at which redside dace maintain equilibrium, providing a powerful tool for understanding how thermal stress affects individual performance. CTmax and TSM of redside dace were sensitive to changes in temperature, regardless of season, suggesting that temperature pulses caused by climate change or urban activities can impose negative fitness consequences year round. Interestingly, an individual's recent thermal history was more influential to its thermal tolerance than the current ambient water temperature. While the CTmax of redside dace increased with body size, the effect of body size on TSM remains unclear based on our models. The results provide insight into the thermal performance of redside dace that, to date, has been difficult to assess due to the species' rarity and lack of suitable streamside protocols.

Application of multiple-population viability analysis to evaluate species recovery alternatives

Population viability analysis (PVA) is a powerful conservation tool, but it remains impractical for many species, particularly species with multiple, broadly distributed populations for which collecting suitable data can be challenging. A recently developed method of multiple-population viability analysis (MPVA), however, addresses many limitations of traditional PVA. We built on previous development of MPVA for Lahontan cutthroat trout (LCT) (Oncorhynchus clarkii henshawi), a species listed under the U.S. Endangered Species Act, that is distributed broadly across habitat fragments in the Great Basin (U.S.A.). We simulated potential management scenarios and assessed their effects on population sizes and extinction risks in 211 streams, where LCT exist or may be reintroduced. Conservation populations (those managed for recovery) tended to have lower extinction risks than nonconservation populations (mean = 19.8% vs. 52.7%), but not always. Active management or reprioritization may be warranted in some cases. Eliminating non-native trout had a strong positive effect on overall carrying capacities for LCT populations but often did not translate into lower extinction risks unless simulations also reduced associated stochasticity (to the mean for populations without non-native trout). Sixty fish or 5-10 fish/km was the minimum reintroduction number and density, respectively, that provided near-maximum reintroduction success. This modeling framework provided crucial insights and empirical justification for conservation planning and specific adaptive management actions for this threatened species. More broadly, MPVA is applicable to a wide range of species exhibiting geographic rarity and limited availability of abundance data and greatly extends the potential use of empirical PVA for conservation assessment and planning.

Ecological Status of Juglans cinerea in New Brunswick

Butternut (Juglans cinerea L.), an early successional riparian hardwood species native to Canada and the United States, is under serious threat from a nonnative fungal pathogen, Ophiognomonia clavigignenti-juglandacearum. Since it was first reported in Canada in 1990, this fungal pathogen has spread rapidly and established in New Brunswick in 1997. Apart from the first report in 1997 and another in 2004, no surveys have been conducted to assess the spread of the pathogen in the province. The purpose of this research was to survey butternut throughout its range in New Brunswick, evaluate disease occurrence as well as tree health, and investigate the impact of different topographic and tree health factors on canker incidence. Results showed that the disease has spread throughout the range of butternut in New Brunswick. The disease likely only recently (2007) spread to the northeastern-most populations, given that lower rates of canker occurrence and higher health ratings are found further away from the point of initial occurrence of the disease. Although canker incidence is high throughout the province, tree dieback is minimal, and trees still producing nuts could support opportunities for ex situ conservation. Because of the rate of pathogen spread in the province, implementing a tree improvement strategy might be the only means for maintaining the butternut genome on the landscape.

Vegetation structure and ground cover attributes describe the occurrence of a newly discovered carnivorous marsupial on the Tweed Shield Volcano caldera, the endangered black-tailed dusky antechinus (Antechinus arktos)

The black-tailed dusky antechinus (Antechinus arktos) is a recently discovered, endangered, carnivorous marsupial mammal endemic to the Tweed Shield Volcano caldera, straddling the border between Queensland and New South Wales in eastern Australia. The species' preference for cool, high-altitude habitats makes it particularly vulnerable to a shifting climate as these habitats recede. Aside from basic breeding and dietary patterns, the species' ecology is largely unknown. Understanding fine-scale habitat attributes preferred by this endangered mammal is critical to employ successful conservation management. Here, we assess vegetation attributes of known habitats over three sites at Springbrook and Border Ranges National Parks, including detailed structure data and broad floristic assessment. Floristic compositional assessment of the high-altitude cloud rainforest indicated broad similarities. However, only 22% of plant species were shared between all sites indicating a high level of local endemism. This suggests a diverse assemblage of vegetation across A. arktos habitats. Habitat characteristics were related to capture records of A. arktos to determine potential fine-scale structural habitat requirements. Percentage of rock cover and leaf litter were the strongest predictors of A. arktos captures across survey sites, suggesting a need for foraging substrate and cover. Habitat characteristics described here will inform predictive species distribution models of this federally endangered species and are applicable to other mammal conservation programs.

Thermal tolerance depends on season, age and body condition in imperilled redside dace Clinostomus elongatus

Urbanization tends to increase water temperatures in streams and rivers and is hypothesized to be contributing to declines of many freshwater fishes. However, factors that influence individual variation in thermal tolerance, and how these may change seasonally, are not well understood. To address this knowledge gap, we studied redside dace Clinostomus elongatus, an imperilled stream fish native to rapidly urbanizing areas of eastern North America. In wild redside dace from rural Ohio, USA, acute upper thermal tolerance (i.e. critical thermal maximum, CTmax) ranged between ~34°C in summer (stream temperature ~22°C) and 27°C in winter (stream temperature ~2°C). Juveniles had higher CTmax than adults in spring and summer, but in winter, CTmax was higher in adults. Thermal safety margins (CTmax - ambient water temperature; ~11°C) were less than the increases in peak water temperature predicted for many redside dace streams due to the combined effects of climate change and urbanization. Furthermore, behavioural agitation occurred 5-6°C below CTmax. Safety margins were larger (>20°C) in autumn and winter. In addition, redside dace were more sensitive (2.5°C lower CTmax) than southern redbelly dace Chrosomus erythrogaster, a non-imperilled sympatric cyprinid. Body condition (Fulton's K) of adult redside dace was positively correlated with CTmax, but in juveniles, this relationship was significant only in one of two summers of experiments. Next, we measured CTmax of captive redside dace fed experimentally manipulated diets. In adults, but not juveniles, CTmax was higher in fish fed a high- vs. low-ration diet, indicating a causal link between nutrition and thermal tolerance. We conclude that redside dace will be challenged by predicted future summer temperatures, especially in urbanized habitats. Thus, habitat restoration that mitigates temperature increases is likely to benefit redside dace. We also suggest habitat restoration that improves food availability may increase thermal tolerance, and thus population resilience.

Reduced genetic diversity and low effective size in peripheral northern European catfish Silurus glanis populations

Using 10 polymorphic microsatellites and 1251 individual samples (some dating back to the early 1980s), genetic structure and effective population size in all native and introduced Swedish populations of the European wels catfish or Silurus glanis were studied. Levels of genetic variability and phylogeographic relationships were compared with data from a previous study of populations in other parts of Europe. The genetically distinct Swedish populations displayed comparably low levels of genetic variability and according to one-sample estimates based on linkage disequilibrium and sib ship-reconstruction, current local effective population sizes were lower than minimum levels recommended for short-term genetic conservation. In line with a previous suggestion of postglacial colonisation from a single refugium, all Swedish populations were assembled on a common branch in a star-shaped dendrogram together with other European populations. Two distinct subpopulations were detected in upper and lower habitats of River Emån, indicating that even minor dispersal barriers may restrict gene flow for wels in running waters. Genetic assignment of specimens encountered in the brackish Baltic Sea and in lakes where the species does not occur naturally indicated presence of long-distance sea dispersal and confirmed unauthorised translocations, respectively.

DNA Sequence Variants and Protein Haplotypes of Casein Genes in German Black Pied Cattle (DSN)

Casein proteins were repeatedly examined for protein polymorphisms and frequencies in diverse cattle breeds. The occurrence of casein variants in Holstein Friesian, the leading dairy breed worldwide, is well known. The frequencies of different casein variants in Holstein are likely affected by selection for high milk yield. Compared to Holstein, only little is known about casein variants and their frequencies in German Black Pied cattle (“Deutsches Schwarzbuntes Niederungsrind,” DSN). The DSN population was a main genetic contributor to the current high-yielding Holstein population. The goal of this study was to investigate casein (protein) variants and casein haplotypes in DSN based on the DNA sequence level and to compare these with data from Holstein and other breeds. In the investigated DSN population, we found no variation in the alpha-casein genes CSN1S1 and CSN1S2 and detected only the CSN1S1*B and CSN1S2*A protein variants. For CSN2 and CSN3 genes, non-synonymous single nucleotide polymorphisms leading to three different β and κ protein variants were found, respectively. For β-casein protein variants A¹, A², and I were detected, with CSN2*A¹ (82.7%) showing the highest frequency. For κ-casein protein variants A, B, and E were detected in DSN, with the highest frequency of CSN3*A (83.3%). Accordingly, the casein protein haplotype CSN1S1*B-CSN2*A¹-CSN1S2*A-CSN3*A (order of genes on BTA6) is the most frequent haplotype in DSN cattle.

Notes on the sinistral helicoid snail Bertia cambojiensis (Reeve, 1860) from Vietnam (Eupulmonata, Dyakiidae)

Since the time of the original description there have been no precise locality records in Cambodia of Bertia cambojiensis (Reeve, 1860) and it was believed to be extinct. In 2012, a joint Natural History Museum survey with Vietnamese colleagues rediscovered living populations of this huge sinistral helicoid snail in a protected area of southern Vietnam. The genitalia and radula morphology are re-assessed and type specimens of all recognised congeners are figured herein. The unique morphological characters of this species are a small and simple penis, well-developed amatorial organ complex that incorporates four amatorial organ ducts, a short gametolytic organ complex and spiked papilla, and radula morphology with unicuspid teeth. The type locality of B. cambojiensis, which has been contentious, is determined here to be in the vicinity of 'Brelum', Vietnam, near the border with Cambodia. In addition, the nucleotide sequences of barcoding genes COI, 16SrRNA and 28S fragments were provided for further comparison.

Breeding Centers, Private Ranches, and Genomics for Creating Sustainable Wildlife Populations

Human-induced changes to environments are causing species declines. Beyond preserving habitat (in situ), insurance (ex situ) populations are essential to prevent species extinctions. The Conservation Centers for Species Survival (C2S2) is leveraging space of breeding centers and private ranches to produce “source populations”—genetically diverse reservoirs that also support research and reintroductions. The initial focus is on four African antelopes. C2S2 has developed a program, the Source Population Alliance, that emphasizes animals living in spacious, naturalistic conditions in greater numbers than can be accommodated by urban zoos. Simulation modeling demonstrates how herds can rapidly increase population abundance and retain genetic diversity. Advances in genomics and resulting DNA data allow monitoring of genetic diversity and parentage as well as refined decision-making. This approach, neither pure in situ nor ex situ, but rather “sorta situ”, is an innovative way of linking public and private sector resources to ensure that endangered species survive.

Using Noninvasive Genetic Sampling to Survey Rare Butterfly Populations

Advances in nondestructive genetic sampling techniques continue to offer new opportunities for studying organisms, particularly those of conservation concern where more traditional invasive sampling methods are often not available. As part of a proof-of-concept, we investigated the effectiveness of using the chorion from residual butterfly egg debris as a source of viable genetic material for analysis. Laboratory material from a captive breeding population of the federally endangered Miami blue butterfly (Cyclargus thomasi bethunebakeri) was used to test efficacy and refine the methodology. The resulting best practices were subsequently evaluated using field-collected material from extant north Florida populations of the at-risk frosted elfin butterfly (Callophyrs irus). Our results demonstrated that it is possible to extract DNA of sufficiently high quantity and quality for successful gene sequencing. We additionally describe a simple, low-cost, and reliable method of collecting and storing egg debris samples that can be consistently adopted for field or laboratory work as well as deployed with projects that have a larger geographic scope and/or involve citizen scientists. Potential limitations related to field sample collection are discussed as well as needs for future evaluation.